June 9, 2016

Neolithic DNA from Greece and NW Anatolia and their influence on Europe

This is a most interesting study that brings to us potentially key information on the expansion of European Neolithic and the formation of modern European peoples.

Zuzana Hofmanová, Susanne Kreutzer et al., Early farmers from across Europe directly descended from Neolithic Aegeans. PNAS 2016. Open accessLINK [doi:10.1073/pnas.1523951113]

Abstract

Farming and sedentism first appeared in southwestern Asia during the early Holocene and later spread to neighboring regions, including Europe, along multiple dispersal routes. Conspicuous uncertainties remain about the relative roles of migration, cultural diffusion, and admixture with local foragers in the early Neolithization of Europe. Here we present paleogenomic data for five Neolithic individuals from northern Greece and northwestern Turkey spanning the time and region of the earliest spread of farming into Europe. We use a novel approach to recalibrate raw reads and call genotypes from ancient DNA and observe striking genetic similarity both among Aegean early farmers and with those from across Europe. Our study demonstrates a direct genetic link between Mediterranean and Central European early farmers and those of Greece and Anatolia, extending the European Neolithic migratory chain all the way back to southwestern Asia.



Uniparental DNA

One of the most important findings is that the two Epipaleolithic samples from Theopetra yielded mtDNA K1c, being the first time in which haplogroup K has been detected in pre-Neolithic Europe. Sadly enough these two individuals could not be sequenced for full genome. 

The other five individuals are all Neolithic (three early, two late) and did provide much more information.
  • Rev5 (c. 6300 BCE): mtDNA X2b
  • Bar31 (c. 6300 BCE): mtDNA X2m, Y-DNA G2a2b
  • Bar8 (c. 6100 BCE): mtDNA K1a2
  • Pal7 (c. 4400 BCE): mtDNA J1c1
  • Klei10 (c. 4100 BCE): mtDNA K1a2, Y-DNA G2a2a1b (same as Ötzi's)
I color coded their abbreviated names according to the usage in the study's many maps, for easier reference: green shades are for Greece (Western Macedonia), red shades for Turkey (Bursa district). It is also very convenient to get straight their real geography because many of the map-styled graphs are not precise at all about that:

Fig. 1.
North Aegean archaeological sites investigated in Turkey and Greece.



Autosomal DNA affinities

This is probably the most interesting part. There is a lot about it in the supplementary information appendix but I find that the really central issue is how they relate to each other (or not) and to other ancient and modern Europeans. I reorganized figs S21 and S22 to better visualize this:


Ancient samples compared to each other and other ancient samples ("inferred proportions of ancestry")
Ancient samples compared to modern Europeans ("inferred proportions of ancestry")


So what do we see here? First of all that the strongest contribution of known Aegean Neolithic peoples on mainline European Neolithic is from Bar31, which is from NW Anatolia, and not from Greece. Bar8 is a less important contributor but may have impacted particularly around the Alps (Stuttgart-LBK, modern North Italians).

This goes against most archaeology-based interpretations, which rather strongly suggest a Thessalian and West Macedonian origin of the Balcanic and, therefore, other European branches of the mainline Neolithic of Aegean roots, and do instead support some sort of cultural barrier near the European reaches of the Marmara Sea. Of course we lack exhaustive sampling of Greek Neolithic so far, so it might be still possible that other populations from Thessaly or Epirus could have been more important. However the lack of Anatolian-like influence on the Western Macedonian Neolithic until c. 4100 BCE, makes it quite unlikely.

So it seems that, once again, new archaeogenetic information forces us to rethink the interpretative theories based on other data.

However we do see a strong influence of Greek Neolithic and particularly the oldest sample, Rev5, in SW Europe, very especially among Basques, who seem to have only very minor Anatolian Neolithic ancestry, unlike everyone else relevant here. This impact is also apparent in Sardinia and to some extent North Italy (but overshadowed in these two cases by the one from Anatolia, particularly Bar31).

There are also similar analyses for other four ancient samples (Lochsbour, Stuttgart, Hungary Neolithic and Hungary Bronze) but they don't provide truly new information, so I'm skipping them here. As I said before, there's a hoard of analyses in the SI appendix, enjoy yourselves browsing through them and feel free to note in the comments anything you believe important.

A synthesis of the various "inferred proportions of ancestry" analyses is anyhow shown in fig. 3:

Fig. 3. (click to expand)
Inferred mixture coefficients when forming each modern (small pies) and ancient (large pies, enclosed by borders matching key at left) group as a mixture of the modern-day Yoruba from Africa and the ancient samples shown in the key at left.

The fractions may be misleading however, especially for the ancients. For example: Lochsbour (a total outlier among the ancients in this study) appears best correlated with Pal7 but in fig. S24 it is clear that does no correlate with any Neolithic sample at any significant level. But in general terms it can give a good idea of where does ancestry, particularly for modern samples, come from.

Note: elsewhere someone was being a crybaby about the Polish sample (may well be an error) or the Kalmyk sample (who are obviously most related to East Asians, not used here) but those are minor issues.

Of course there's a lot more to learn from the remains of the ancients. Let's keep up the good work.

27 comments:

  1. Hi Maju, this might interest you.

    "The genetic structure of the world's first farmers" (Natufians)
    http://www.biorxiv.org/content/early/2016/06/16/059311

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  2. Kaixo Maju: There are two articles in Eurogenes about Natufian DNA and "The genetics of early neolithic pastoralist from western Iran" that might interest you.
    I am expecting your commentaries.

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  3. Thank you both for the heads up. I'm not anymore paying as strong attention to RSS, etc., so your direct feed is important. I'm also not writing as much, as you probably noticed. Sorry about that but, as my brother always reminds me: if you're not paid for it, it's a hobby, so take it easy.

    First impressions:

    1. High differentiation between Palestine and Kurdistan Neolithic peoples - as I expected.

    2. High "basal Eurasian" in Palestine Neolithic - as I expected. Interesting that it is associated with lower Neanderthal component.

    3. farmers related to those of Anatolia spread westward into Europe; farmers related to those of the Levant spread southward into
    East Africa; farmers related to those from Iran spread northward into the Eurasian steppe; and people related to both the early farmers of Iran and to the pastoralists of the Eurasian steppe spread eastward into South Asia
    . Pretty interesting, really.

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  4. Another thing: fig. 1b (and 1c as well) illustrates that my old idea that the European Neolithic links to Levant Neolithic is not far fetched. The "blue" component is primarily Natufian/Levant Neolithic and Anatolian Neolithic peoples rather seem intermediate between these Levant Neolithic peoples and Early/Late European Farmers. It'd be interesting to have samples from the area in between: South-Central Anatolia, Cyprus and North Levant (Syria, Lebanon) but seems that the time has not come yet.

    My hypothesis, just for the record is that the pre-EEF origins would be in the North Levant, arriving, via Cyprus and maybe the coasts but not the interior of Southern Anatolia, to West Anatolia and Greece, where they mixed with peoples related to WHG. That it was a primarily naval/coastal migration of highly mobile fisher-farmers.

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  5. Hi Maju, the most important piece of the paper to me is,

    "However, no affinity of Natufians to (ancient nor modern) sub-Saharan Africans is evident in our genome-wide analysis, as present-day sub-Saharan Africans do not share more alleles with Natufians than with other ancient Eurasians"

    "Further insight into the origins and legacy of the Natufians could come from
    comparison to Natufians from additional sites, and to ancient DNA from north Africa".

    It should officially make haplogroup E, Eurasian in origin. At least until they can come up with older dates for E in the African continent,(period).

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    1. They did not compare with the Dinka or any other Sudanese or Tribal Ethiopian population, which are the must-do comparisons, not Yorubans and which have on occasion produced indications of genetic flow to European Neolithic populations (Skoglund, supp. materials).

      "It should officially make haplogroup E, Eurasian in origin".

      No way! You may argue for a source population with negligible Tropican African ancestry but the lineage comes from Africa 200% sure.

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    2. actually we have no way of knowing the place or population of origin of a haplogroup as old as E is, since people are mobile and also able to breed across population boundaries. Besides, we have a 4500 year old African with no evidence of Eurasian admixture carrying the same haplogroup, so there is no way to tell.

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    3. Actually we can pinpoint with great precision the origin of every single haplogroup by using common sense or, more precisely: the geostructure or the geography of the phylogeny. IF a lineage X arose in region A, it will have left with extremely high probability a hoard of rare basal lineages in that region and not in other regions, because in each migration a founder effects happen reducing the diversity. The basal diversity of E is unmistakably in Africa, towards the Upper Nile and that of DE is also in Africa, as happens with its precursors BT and AT. The only doubtful point is CT, because half (DE) is most basally diverse in Africa and the other half (CF) is clearly an Asian haplogroup but that seems to respond to a peculiar moment of high mobility: the Abbasia Pluvial and the relate Out-of-Africa migration.

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    4. that's precisely what i doubt. Haplogroup E may well have originated in Southern Arabia and been virtually obliterated there by the expansion of haplogroup J subclades, with the basal diversity around the Upper Nile being just a preservation artifact.

      About testing African affinities of Natufians using Tribal Ethiopians, well, they used Mota which is basically Ari minus the West Eurasian part. It showed no affinity to Natufians.

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    5. It MIGHT but chances are so slim and evidence so clearly non-existent that we can safely discard that idea. Also South Arabia (Yemen) was invaded by Neanderthals with Mousterian technology c. 70.000 BP, reinforcing the divide between the African and Asian subsets of Humankind.

      If there's anything to that "Basal Eurasian" thingy, it should be related to Y-DNA G and not to E. Also it should be more centered towards Iran, where it's possible (although unproven as of now) that pockets of OoA early populations might have survived in the Persian Gulf "oasis" (then an emerged marshy area).

      Re. Mota and Dinka, I think that there was Afro-Eurasian admixture in the Nile Valley since c. 50 or 45 Ka BP (LSA genesis and other UP-related developments), hence the migration of Y-DNA E to NW Africa or Asia must have happened within already admixed populatons, for whom the isolated Mota sample is not a good proxy, sadly enough. The Dinka may be instead.

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    6. Another thing: the insistence, against all evidence and without a single indication in favor, on claims that Y-DNA E to have originated outside Africa is, I am pretty sure, a racist claim. You may or not be aware of the implicit racism in defending what can only be considered pseudoscience (no evidence, just blind faith) on no reason at all, other that it happens to make Europeans and West Asians a bit African ourselves.

      Guys, please, get over your Nordicist racist bias: racism is bad for intelligence.

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    7. ok, i didn't know Arabia had been occupied by Neanderthals at the relevant time frame. As to "Basal Eurasian", i wasn't thinking specifically about it, but rather in terms of three possible sources for E:

      1) An Eurasian (including "Basal Eurasian") source

      2) A source closely related to modern Africans

      3) A source basal to Eurasians (including "Basal Eurasians") which would have not left much of an autosomal signature in modern populations.

      As for using the Dinka to test Natufian affinities, if they are WEA admixed, won't they confound the analysis?

      Lastly: yes, i'm aware that people pushing for an Eurasian origin for haplogroup E tend to hold a certain contempt towards Africans. Anyway, the whole thing is a bit silly, given that haploid markers of clear African origin are found at low frequencies among modern Europeans.

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    8. Re. Mousterian Yemen: http://forwhattheywereweare.blogspot.com/2012/07/late-middle-paleolithic-industry-of.html

      Re. Dinka, see this image (or other similar ones): http://i.imgur.com/3BDeuRm.png

      Contrary to Maasai, who do seem to have a minor WestAsian admixture (light green), Dinka have it not, being exclusively African in their makeup: mostly East African (pink), secondarily West African (orange) and very minor traces of Mbuti component (dark green). This seems common in South Sudan.

      Also the trees I have seen show proto-Dinka contribution to some EEF types (Ötzi if I recall correctly) and not the other way around. The chance of confusion using Dinka as control is almost zero. However they are surely not the contributor population but a related and "more Eurasian" one like Nubians or pre-Neolithic Egyptians. Notice that there are Asian-derived haplogroups that are very very old in NE Africa, like mtDNA X1 and M1, but also Y-DNA J1 and T with all likelihood. Asian peoples must have back-migrated to Africa (NE) around 50-40 Ka ago, at about the same time they were migrating to Europe and Altai, with UP technology, that in Africa is usually known as LSA (Late Stone Age). So the population that back-migrated (again) to Palestine and maybe other areas, must have been already admixed with Asian and even specifically European blood (this one probably arrived via Morocco). I think it's very unrealistic to imagine Mesolithic Egyptians and Nubians as pure unadmixed full blooded Africans. They were already a mix with Y-DNA E1b but also J1, which is very very diverse in the Nile Valley and must have arrived to Ethiopia and NW Africa prior to Neolithic from that origin (in NW Africa it should be attributed to Capsian culture).

      I think there may be at least two "Basal Eurasian" sources: one, admixed with "true African" blood, in Egypt and Nubia, which clearly influenced the Mesolithic of Palestine, and another, maybe "true Asian" but "pre-Indian" ("Paleoarabian") possibly refuged in the Persian Gulf Oasis but surely also implanted in the mountains north of it, as suggested by Iran-Neolithic and Caucasus Epipaleolithic genetics.

      "i'm aware that people pushing for an Eurasian origin for haplogroup E tend to hold a certain contempt towards Africans".

      Yeah, it's like Brexit: almost nobody will admit but it's all about racism, just different shades of it.

      "the whole thing is a bit silly"

      Maybe but it's all about denying that Africa played even a minor role in the genesis of civilization, when it actually did, particularly the area of Egypt-Nubia, which is clearly inside the Fertile Crescent, at least some more honest versions of it.

      "haploid markers of clear African origin are found at low frequencies among modern Europeans".

      Indeed. We are all a bit "black". East and South Asians probably not but Europeans definitely yes.

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    9. ok, but the findings on Yemen are just some stone tools for what I see, no human remains so we don't know who was there.

      And also, doesn't that pink "East African" component contain some traces of specifically West Eurasian affinity? it seems so to me from the whole Admixture runs i have seen.

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    10. Never ever Mousterian has been associated with any other human species. Mousterian means Neanderthals unless you can prove it otherwise.

      "doesn't that pink "East African" component contain some traces of specifically West Eurasian affinity?"

      No that I can discern. Maasai have "traces" of West Eurasian admixture and in that graph they appear very clear in the same color as the Bedouin component.

      Anyhow, traces should not affect the analysis in any significant way.

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    11. Well, it seems the Skuhl/Qafzeh remains were associated with mousterian tools and those people were not Neanderthal, rather they seem like the earliest modern humans Out of Africa. So i'm not sure mousterian= neanderthal.

      as for West Eurasian affnities of that East African component, it shows on the admixture run on haak et al 2014. The Dinka show some of the orange component associated with Neolithic Europeans until a component associated with them and several other East African populations appears.

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    12. I remember discussing the matter with a Neanderthalist professor back in the day and my memory was that the issue was pretty clear. I'm not certain that the Skuhl/Qafzeh remains are associated with Mousterian tools, although they were associated with perforated shells that have been considered by some the oldest known "symbolic behavior", also found in NW Africa (Aterian, no Neanderthal relationship at all) and at a later date in Southern Africa (MSA, also Sapiens-related). However Skuhl 5 particularly has always been a strong candidate for early Neanderthal admixture and Neanderthals are known to have been living just north of those sites, in Syria.

      I'll leave it at that.

      "The Dinka show some of the orange component associated with Neolithic Europeans until a component associated with them and several other East African populations appears."

      That would also support my "Dinkaist" or "Nubianist" stand. EEFs are the first population in which the ghostly Basal Eurasian element was located. It's only natural that Dinka show some affinity to them if the BEA component came from Nubia.

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    13. yeah, skuhl 5 certainly looks Neanderthal admixed. And the orange stuff in Dinka could be interpreted any way, admitedly.

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  6. you might be interested in this (if you haven't seen it already)

    https://link.springer.com/article/10.1007/s10963-016-9093-0

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    1. It looks very interesting: all about Irish prehistory or almost. Thank you.

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  7. @Maju, it's just a thought, nothing concrete, but this study just came out yesterday.

    "Admixture into and within sub-Saharan Africa"

    https://elifesciences.org/content/5/e15266/article-data#fig1

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    1. This comment has been removed by the author.

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    2. Well, it has some interest but doesn't really tell us something we don't know (other than chronological speculations, hard to understand), does it?

      I'm putting it in my "to do" list, which, sadly enough is full of papers and articles I never got to comment. I have other priorities right now, particularly the new Lazaridis paper.

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  8. I've been waiting for your discussion of the Lazaridis paper, and wanting to add my own observations (predictions). Can't wait to comment any more so am doing it here.


    It seems to me as if Lazaridis' paper is just the build up to Harvard's South Central Asia/South Asia paper. They seemed to have taken a brief detour to recalibrate Yamna to use up some Iranian Neolithic, as the other guys (the Lopez abstract) claimed Iranian Neolithic to be significant in the South (Central) Asia region. The fact that Harvard's scrubbed CHG and replaced it with Iran Neolithic, while everyone else is still arguing for CHG in South (Central) Asia, seems to fit with how they know their data of the upcoming region in advance, while the rest don't. So they know what to tweak beforehand.

    This is my theory: the statistics predicting admixture in South (Central) Asia of Iran Neolithic and the early steppe, rather than the later steppe as was anticipated (by means of Sintashta or Andronovo), may be because the (proto-)BMAC will turn out to already be a match and have to be compensated for. Perhaps the data even shows some BMAC input into Sintashta and Srubna and even Maykop. So by claiming the South (Central) Asia region already had steppe ancestry from the eneolithic or early bronze age, since the Iran Neolithic presence in the region is likely and straightforward in the comparison, (proto-)BMAC will get subsumed under steppe origins and become a steppe culture in entirety too. And after that it won't even matter that the Sintashta or Srubna were partially derived from them, since BMAC would by then have been presented as a part of the steppe horizon since inception.

    If this all turns out to be the case, I think BMAC will be made the Indo-Iranian urheimat, but it will now have changed hands to being a steppe culture, and therefore be a West-Eurasian culture. It won't really be a win for South Central Asians, as BMAC will be now be rewritten to belong to European origination as much as Sintashta if not more so. Sort of like heads I win tails you lose anyway. They've prepared the case for however it turns out, though the Iranian Neolithic in Yamna seems to indicate they have some inkling of how it will pan out. People like Nirjhar will be "right" but gain nothing from it any way as others will still get credited. Before, BMAC was not IE but "native" and could only be invaded by Sintashta, and now it will be spun the other way if found to have influenced the steppes to its north: BMAC would be steppe not native in origins (and only then does it get to be IE). The insistence lies in the dichotomy that IE cannot belong to the region and must be European euphemized to West-Eurasian.

    I may well be wrong, but if I turn out to be right then it's purely because it was an artificial foreshadowing, rather than because of the arguments and stats in Lazaridis being used genuinely predictively. Which they can't really be, since the Harvard guys surely must have the South (Central) Asian aDNA already and have analyzed it already too. I hope I'm wrong though. Because otherwise it looks more planned and constructed than like research. Sort of like how CHG was "apparently genetically isolated" in the Jones 2015 paper, whereas in the Lazaridis paper the upper paleolithic Caucasus Hunter Gatherers are shown as an admixture that involves later (neolithic) Iranian genomes. CHG went from a perfect match for admixture into Yamna to not the perfect match, proportional to the rise in prominence of Iran Neolithic's significance in South (Central) Asia, almost as if that was the target and the rest was just to compensate to reach it. If Iran Neolithic had not turned out to be so significant in South (Central) Asia and in Iranian Zoroastrians, Harvard may perhaps not have bothered to replace the CHG in Yamna with Iran Neolithic. It's whatever their target population has that they need to match it with. It shifts with the goal.

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    Replies
    1. Go and write a blog, you are much more enthusiastic and non-distracted than I am! Hahahaha! I just spent all night watching the English vote come out via the Net, Anthropology can wait when the World is Chaos-dancing. I'll see to write something this weekend, because Sunday Night and Monday is busy too counting an evaluating Spanish votes.

      I don't think that we can infer too much from the paper re. Central Asia, because we lack of local ancient samples and Onge are not a good proxy at all, not even a bit better than other SE Asians, probably worse. In such a situation the tendency is for the test population to adhere to "random others", which are meaningless or almost. In fact I did not plan to make but a passing mention to South Asia: the data is not yet there.

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  9. Hi Maju: Something new for you.

    http://www.cell.com/current-biology/fulltext/S0960-9822(16)30850-8

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    1. Oooh! Thank you very much, Olga. :)

      Very interesting. First quick thoughts:

      1. Notable amounts of mtDNA N1a1a1, the exact same lineage found in Derenburg and other locations of East Germany's Danubian Neolithic, which was argued by Palanichamy 2010 to be European specific but now seems not quite that. Vide: http://www.biomedcentral.com/content/pdf/1471-2148-10-304.pdf

      2. A very Cypriot-like projection of the autosomal data for these and other Anatolian Neolithic farmers, quite distinct from modern Turks, who appear more displaced towards the North. While projection is always a bit problematic, it would seem that the midline between these ancient South Anatolian farmers and the WHG (Magdalenian-derived) populations is right on modern Spaniards. Other than Basques, Spaniards and Sardinians, European populations are, like Turks, drifted to the North/NE (although let's not forget that dimension 2 is always smaller and in this case MUCH smaller than dimension 1, so distances in that axis appear to be comparatively much greater than they really are, I'm talking of fig. 2).

      I'll write something this weekend. Thanks again.

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