June 26, 2016

Ancient genomes from Neolithic West Asia

This week we got to know a lot more about the genetics of ancient West Asians, from the Mesolithic, Neolithic and later times. All in a single major study:

Iosif Lazaridis et al., The genetic structure of the world's first farmers. BioRxiv 2016. Freely accessible (pre-pub)LINK [doi: http://dx.doi.org/10.1101/059311]

Abstract

We report genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000-1,400 BCE, from Natufian hunter-gatherers to Bronze Age farmers. We show that the earliest populations of the Near East derived around half their ancestry from a 'Basal Eurasian' lineage that had little if any Neanderthal admixture and that separated from other non-African lineages prior to their separation from each other. The first farmers of the southern Levant (Israel and Jordan) and Zagros Mountains (Iran) were strongly genetically differentiated, and each descended from local hunter-gatherers. By the time of the Bronze Age, these two populations and Anatolian-related farmers had mixed with each other and with the hunter-gatherers of Europe to drastically reduce genetic differentiation. The impact of the Near Eastern farmers extended beyond the Near East: 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.

Highlights:

  • There were (at least) two clearly distinct populations in West Asia in the Mesolithic and Early Neolithic times.
  • Both populations contributed to the West Anatolian farmers that are precursors of the settlers of Neolithic Europe.
  • The so-called "Basal Eurasian" component is not yet clarified if it is something local or admixture with Africans or both. However it is clear that it is associated with reduced Neanderthal admixture.
  • West Eurasian genetic composition can be now understood quite well as the mixture from four sources: two West Asian ones, favored by the Neolithic revolution, and two Paleo-European ones.

This graphic shows pretty well how the ancient populations of West Eurasia are expressed as a mixture of those four founder populations:


That is if you can get through the nomenclature, which is inherited in many cases from a long array of recent studies. I'm not even sure myself in many cases what samples exactly and where from are thrown in each category. But the most important part is that Iran_N and Levant_N are the two Neolithic-specific founder populations of the Fertile Crescent (yeah, N stands for "Neolithic", not "North") and that the other two founder populations from pre-Neolithic Europe are WHG (Epi-Magdalenian peoples from Western and Central Europe) and EHG (Eastern European hunter-gatherers, of Epigravettian culture and maybe even proto-Uralic in one case).

Then we see in the case of Europe how:

1. Anatolia_N (precursors of mainline European Neolithic) are a mix of both West Asian farmer groups, plus a sizable fraction of Western Paleo-european ancestry already.

2. This fraction of Western Paleoeuropeanness increases as the farmers expanded into Europe (EN) and then as there was probably some backflow of Western origins in relation to Megalithism and Bell Beaker (MNChL). But in general remains the same basic genetic composition and in no known case incorporates any Eastern Paleoeuropean component at all, not yet.

3. It is only with the Indoeuropean ("Kurgan") invasions reflected in the category LNBA, when the EHG component begins feeling very important in Europe. If I'm correct, all those samples are from Germany other areas of Central and North Europe, with the Iberian and Italian ones of similar chronology placed in the MNChL tag instead. The LNBA/MNChL contrast is not a strictly chronological analysis but an analysis by categories of ancestry that do overlap in time.

4. In Armenia instead, we see a decrease of the minor EHG component but then an increase in the MLBA ("middle and late Bronze Age") when Armenians arrive from the Balcans and Phrygia, conquering the pre-existing Hurro-Urartean peoples (whose language was probably related to Chechen and other NE Caucasian languages), which should correspond to the formation of Urartu and more specifically to the Hayasa-Azzi and Shupria stages, both considered Urartean (Hurrian). The WHG and Levant-N components we see since the Chalcolithic is similar to what we see in West Anatolia and probably reflect interactions corresponding to Central-Eastern Anatolia, Kurdistan and Syria, for which we have no direct ancient data yet.

Ancient samples (colored and labeled) projected on a PCA of modern West Eurasian populations (in gray):


For a reference on which are the modern populations in gray, a good reference is this older but fully labeled PCA by Olalde.

Briefly: Natufians fall on top of modern Palestinians, their slightly admixed Neolithic descendants fall between Palestinians and Jews, Middle Neolithic European Farmers fall on top of Sardinians, the so-called Europe-Steppe continuum (early Western Indoeuropeans) fall between Central Europe, France and the Balcans, most Western Europeans do not overlap with ancient samples but appear to have even greater Paleoeuropean admixture instead, etc.

Y-DNA Haplogroups

Iranian Mesolithic and Neolithic samples carried the following patrilineages:
  • Mesolithic: J(xJ2a1b3,J2b2a1a1)
  • Ganj Dareh Neolithic: P1(xQ,R1b1a2,R1a1a1b1a1b,R1a1a1b1a3a,R1a1a1b2a2a) and an undefined CT
  • Late Neolithic: G2a1(xG2a1a)

Meanwhile Palestinian Mesolithic and Neolithic samples carried: 

  • Natufian (Mesolithic): E1b1b1b2(xE1b1b1b2a,E1b1b1b2b), E1b1(xE1b1a1,E1b1b1b1), E1b1b1b2(xE1b1b1b2a,E1b1b1b2b), plus two undefined CT.
  • Pre-Pottery Neolithic B/C: H2, E(xE2,E1a,E1b1a1a1c2c3b1,E1b1b1b1a1,E1b1b1b2b), E1b1b1, T(xT1a1,T1a2a), E1b1b1(xE1b1b1b1a1,E1b1b1a1b1,E1b1b1a1b2,E1b1b1b2a1c), plus three ill-defined CT.

CT is the main pan-Eurasian macro-haplogroup and is not informative, except in Palestine because it implies exclusion of E.

Otherwise we see an important presence of E (mostly E1b1b) a lineage we know was carried by early farmers into Europe and that has ultimately African origins. It probably indicates migration of NE Africans into Palestine in the Mesolithic, something also supported by Archaeology. However these NE Africans were surely already mixed with Eurasian ancestry, which probably arrived to the Nile Basin in the early LSA, some 50-40 Ka ago. So it's a complex story of multiple admixture events in the continental crossroads that is Egypt and also Palestine and other nearby areas.

We also see G2a1 in Late Neolithic Iran, and this one is the main lineage brought to Europe by the early farmers if we are to judge on known ancient sequences (today it is not more important that E1b but it is maybe more evenly distributed). However we only see it in the Late Neolithic, so it may have originated further west.

We see too little J, only J(xJ1a,J2a1,J2b) in Chalcolithic Iran and in Bronze Age Jordan: J(xJ1,J2a,J2b2a) again and J1(xJ1a). I guess that a lot remains to be researched on this issue because J is by far nowadays the most common haplogroup of West Asia, and also impacted Europe and South Asia (J2) and North and NE Africa (J1).


On the issue of "Basal Eurasian": African or West Asian?

The question remains unanswered, as I said before but there are two clues: on one side the presence of E1b in Mesolithic and Neolithic Palestine clearly supports a direct NE African influence, also backed by archaeological evidence. But there is some nuance in the issue of FST distances that I want to highlight.

The distances are available in a very extensive supplementary table, so I took just a few to get a better understanding, not only of this issue but in general of the genetic distances of the four founder populations:



Quite ironically it is not the Natufians who are the closest to the African reference population (Yoruba) but the CHG, Iran-N and Levant-N groups. In fact the Natufians are the most distant ones after the WHG population. However this is tricky because the affinity to Yoruba may also be caused by the "ghost" Basal Eurasian population, claimed first of all by Lazaridis 2014, which would be a remnant of the Out of Africa Migration (not strictly African but close enough and impossible to discern from true African admixture in most analyses).

So we may imagine that the "Highlander" (CHG and Iran-N) populations were somehow influenced by that Basal Eurasian ghostly population, which might have survived in the Persian Gulf oasis, for example. Or whatever else.

The presence of the same or similar element in Levant-N reflects possibly admixture with Iran-N or a similar population, something that is implicit in the table above but I'll address below more explicitly.

If there is (and there must be, because of Y-DNA E1b) some African admixture in the Natufian population, it was very diluted already in the autosomal (general DNA) aspect before farming began.

Update (Jul 2): all the four paragraphs above are possibly misleading to some extent because, as several commenters have rightfully pointed out, generic drift alone just causes the effect of increased distance to general reference populations like Yoruba and Han, this genetic drift is caused by relative isolation, so it seems that Magdalenian Europeans (WHG) and Natufian Palestinians (Natufian) were both more isolated populations in general terms than the Iran-Caucasus-Eastern Europe ones, whose sheer numbers apparently kept them more similar to the generic root of Humankind, less endogamous. 

However, per archaeology, such "sheer numbers" are not to be expected in that area, rather the opposite (Western Europe and Palestine are much more richer areas in terms archaeological, suggesting denser populations). So the question remains open as far as I can tell but it should be discerner with more precise tools than mere FST.


A visual of smallest genetic distances between (each "-" represents 0.01 in the table above):

a) Ancient West Asians:

CHG-----IrN-------LeN----Nat
Neolithic peoples of West Asia, even if different, are closer among them than their pre-Neolithic precursors.

b) Pre-Neolithic West Eurasians:

WHG--------EHG----------CHG--------------Nat
The distances between Natufians and everyone else are comparable to those with Han Chinese, however only in the case of the populations that appear to have extra affinity to East Asia (Iran, Caucasus and Eastern Europe), otherwise it is smaller.
All four populations were distant enough from each other to be considered clearly distinctive. Even EHG and WHG were quite dissimilar.

c) The four West Eurasian founders considered above:

WHG--------EHG----------IrN-------LeN
There is much greater similitude between Iran and Levant Neolithic peoples than between their Mesolithic precursors. This implies some sort of intense admixture as agriculture and herding developed. Not enough to erase the differences but enough to blur them significantly.

Genetic influence from East Asia or a related population is also apparent in all Northeastern populations but even more so in Iran Neolithic. Why?

There is much more in the study and supp. materials but I can only review so much.

82 comments:

  1. What do you think about EBA R1b? I find it very intriguing that this sample is less EHG than the Chalcolithic Armenians and MLBA Armenians. Moreover, he has some extra WHG.

    According to Genetiker MLBA Armenian yDNAs are: R1b1a2, E1b1b1b2a1a-L788, R1b1a2a2, J2b2a-Z590, E1b1b1b2a1a-FGC18319/Y5413.

    So you argue that “In Armenia instead, we see a decrease of the minor EHG component but then an increase in the MLBA ("middle and late Bronze Age") when Armenians arrive from the Balcans and Phrygia, conquering the pre-existing Hurro-Urartean peoples (whose language was probably related to Chechen and other NE Caucasian languages).”

    If you take a look at the admixture chart on p. 16 in The Caucasus as an asymmetric semipermeable barrier to ancient human migrations, you see that Armenians are very much Neolithic Near East. They have less North European ancestry than Adyge, Chechens, Lezgins, Balkars, Kumyks and Nogays. Also Georgians and Abkhazians have little North European ancestry but compared to them, Armenians have light blue “Bedouin ancestry”. On the basis of their genetic makeup, Armenians could indeed have come from Anatolia and the Balkans.

    In Neolithic patrilineal signals indicate that the Armenian plateau was repopulated by agriculturalists, it is found that:
    “Of the lineages within haplogroup R, the largely Near Eastern27 R1b1b1*-L23 predominates in Ararat Valley, Gardman and Lake Van (33%, 31% and 32%, respectively). Furthermore, in Ararat Valley we find five individuals belonging to the paraphyletic haplogroup R1b1b*-M269. The Sasun collection, meanwhile, contains comparable distributions of haplogroups R1b1b1*-L23 (15%) and R2-M124 (17%).”
    (http://www.nature.com/ejhg/journal/v20/n3/full/ejhg2011192a.html)

    Time estimate for Armenian R1b is c. 6 kya, so it would be in the Chalcolithic time frame. (http://www.nature.com/ejhg/journal/v20/n3/fig_tab/ejhg2011192t3.html#figure-title)

    However, R1b-L23 is typical of Yamna, so Armenian R1b-L23 may well have originated north of Caucasus but the situation is still puzzling: Anatolia ChL is very low on EHG and if Armenians arrived from Anatolia during the Calcolithic or Early Bronze Age, they probably were very low on EHG and I doubt that R1b-L23 existed there at that time. If it is true that Armenians arrive in the MLBA and were more EHG, I would argue that they came from the North and not from Anatolia.

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    1. "What do you think about EBA R1b?"

      I had not noticed but I've considered, at least since 2009-10, that Armenian and Anatolian R1b is partly West Asian and partly back-migration from Europe (highly derived at the tip of the branches). So the West Asian one I would expect to be there since "always", while the European one should only be there since the Phrygio-Armenians arrived in the Iron Age.

      Now that I consider this, I probably have it wrong the comment on ancient Armenians, as there should be no Armenians proper yet before the Iron Age, earlier it was Hurrian land. I'll fix that.

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    2. "If you take a look at the admixture chart on p. 16 in The Caucasus as an asymmetric semipermeable barrier to ancient human migrations, you see that Armenians are very much Neolithic Near East. They have less North European ancestry than Adyge, Chechens, Lezgins, Balkars, Kumyks and Nogays".

      You must be right. What I attributed to Phrygio-Armenian migration must be attributed to Hurro-Hittite one probably. If nothing else because of the chronology, which is too old to be Armenian.

      "Time estimate for Armenian R1b is c. 6 kya, so it would be in the Chalcolithic time frame."

      No prob with me.

      "However, R1b-L23 is typical of Yamna, so Armenian R1b-L23 may well have originated north of Caucasus".

      Or why not to be ancestral to Volga R1b? After all East European ancient samples (Steppe-gibberish ones) all have strong "Iran-N" component. What is clear is that R1b expanded from West Asia in several directions and that we haven't found it was in Europe before Neolithic. However we haven't found it in West Asia either, not yet, so all options are open.

      Genetics would be a lot less confrontational if people would be less worried about patrilineal genetics, really. I thought we had gone through a "feminist revolution" of sorts in the XX century, but seems we are still in the age of aristocrats in some aspects.

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    3. Edited the Armenian cultures/chronology issue.

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  2. By the way, relative to Yoruba Iran N is no more shifted towards Han than European Neolithics are.

    Fst to Han / Fst to Yoruba

    Anatolia_N 0.821

    Europe_EN 0.806

    Iran_N 0.804

    BedouinA 0.881

    Natufian 0.946
    Something is causing European, Anatolian and Iranian neolithics to be Han-shifted relative to BedouinA and Natufians or something is causing BedouinA and Natufians to be more African-shifted in comparison to Han and the Neolithics. With BedouinA the reason should be as f3 tests say.

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    1. Your data does not fit with the one from the supp. materials table (first excel file I think), unless I made a serious transcription error. Natufian to Han: 0.176. The scale of the figures you provide is different than the ones used in the study and also you only provided one datum, when in the header you seem to announce two Han/Yoruba.

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    2. Please check the supp. table one (I have to go to vote soon, no time right now) and make sure you're not quoting the wrong data, for example the confidence interval, which is above the diagonal.

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    3. Neither of us made an error
      Natufian
      Fst to Han 0.176
      To Yoruba 0.186

      0.176/0.186 = 0.946 (rounded)

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    4. Ah, you were dividing! I don't think you can do that, or rather that dividing would produce any meaningful figure we can analyze.

      You may be implying that the high Fst figures only reflect greater isolation (drift) of the affected populations and that it has no connection with either Africa or East Asia, just a more stable, more diverse baseline, that therefore appears less drifted away from the common root. Is that your point?

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    5. I think high fst figures reflect drift, and that ratios produce meaningful results that can be used to analyze fst. Straight out comparison of fst can produce nonsensical results like EHG being closer to Han than to Karitiana.

      That FstHan/FstYoruba comparison provides results rather simple to interpret: the higher the ratio, the closer a population is to Yoruba relative to Han.

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    6. "nonsensical results like EHG being closer to Han than to Karitiana."

      Well, Fst is not the best tool for sure but shouldn't that reflect that Karitiana are very much drifted away relative to other Eurasians? And also that there has been some genetic exchange through the Altai corridor after the precursors of Native Americans migrated East and then North? After all Mal'ta and such were necessarily interacting with East Asians almost as much as proto-Amerinds and then they were also interacting with ancient Eastern Europeans and NE West Asians, it seems.

      "That FstHan/FstYoruba comparison provides results rather simple to interpret: the higher the ratio, the closer a population is to Yoruba relative to Han."

      Relative to... But why this is not apparent in absolute terms? Can drift alone explain it?

      Also does the relative figure represent Yoruba-like admixture? I don't think it does. If anything it represents lower Han-like admixture, else the absolute figure would also tend to Yoruba.

      I guess the Fst approach is not very good but I was drawn to it by a mention in the bulk of the paper and did not have time to inquire further. There's more stuff in the paper on "Basal Eurasian" in fact, and I may add an update later on, because I reckon that the Fst is not good enough for it.

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    7. @ Shaikorth and Maju:

      I don't know if using FST ratios is sensible because my assumption is extra drift will tend to form a linear addition to the FST term. An example under this assumption:

      Say you have populations A and B, both with FST to Yoruba 0.160 and to Han 0.150. So ratio 0.9375.

      Pop B drifts by an extra FST of 0.02 to both populations (drift adds equally to FST from all other populations). So Yoruba becomes 0.180 and Han 0.170. Those form ratio 0.944.

      The ratio becomes more even, even though B has not actually had any admixture towards Yoruba.

      (Applied to the example, populations with a high level of their own drift - e.g. WHG / Karitiana - will tend to have even ratios. But that doesn't apply if you subtract linear amounts from their FSTs to account for their own drift, then compare the ratios.)

      This depends on whether this assumption (drift adds equally to FST with all populations) holds true though. You may need to ask an actual population geneticist.

      If drift actually does behave as a factor in FST, then it may be more sensible to use ratios after all. I find you get more sensible results from adjusting FST matrices for drift when drift is a linear addition to FST though.

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    8. Yes, you're right, Matt and I'm repenting of having used that very rough method of illustrating things. At the very least I could have been more careful and acknowledge the obvious: it was drift what surely pushed the more isolated populations in Magdalenian Europe and Natufian Palestine apart from everyone. Saikorth made a very good point and you do too. I'll write a disclaimer/update now but rather apologizing than correcting: the world is spiraling into chaos in accelerated form, I don't have too much time for prehistory in the midst of ongoing history. Sorry about that.

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    9. I wrote an update in dark red ink. However a question arose to my mind as I wrote it: how can Paleolithic SW Europeans and Natufians be more drifted than the Caspian-Pontic area, when archaeology is much much richer in the former areas, suggesting much larger population densities (as would naturally correspond to milder climate conditions)? Do we know for a fact that those samples are more drifter or is it just an ad-hoc explanation that doesn't actually work?

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    10. That is an intriguing question. It could be that they (the Natufian / WHG) went through periods of more prolonged drift earlier in history, even if they had a large population during the era immediately prior to the Neolithic.

      Although Fu's paper 2016 would suggest that only a minority of the WHG came from the Magdalenian population, though, and most comes from another population from elsewhere in Europe (where the climate may have been more favourable for an immediate post-Glacial Maximum population boom) so it could be that as well (the main trunk of WHG ancestry was highly drifted, and did not "overwinter" the LGM anywhere which would allow it to maintain high population sizes).

      Admixture also decreases some of the effects of drift in increasing FST to outgroups. Modern Europeans tend to have lesser FST with the Yoruba outgroup than a combination of the FSTs from their putative ancestor populations, and so do Uyghur when compared with Han and Iranian groups. In theory the Pontic Caspian groups may be admixed between "ANE" and WHG.

      It could be that the ANE part of the EHG's ancestry came from a place that experienced less drift during the Ice Age, if it was a widespread group.

      For actual evidence of greater drift, what it's worth, the order of most to least drifted going WHG>CHG>Neolithic (EEF / Anatolia / Iran) would fit with Jones's ROH analysis of the ancient genomes that were robust enough for that -

      http://www.nature.com/ncomms/2015/151116/ncomms9912/images_article/ncomms9912-f3.jpg

      and the same figure from the new paper with same analysis for Iranian Neolithic GD13a - http://i.imgur.com/z6c6QE9.png and http://biorxiv.org/content/biorxiv/early/2016/06/18/059568.full.pdf

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    11. Your links are very intereting, thank you. It suggests that CHG and WHG had very marked founder effects, even sharper than Native Americans. The question is that this happened to both and that in more recent times at least some of the CHG (Satsurbilia but not Kotias) went through a second bottlenecking of some sort (probably drift by isolation, I guess).

      That should make CHG have similar Fst distances to the outgroups as WHG but they are actually much smaller.

      EEFs we can't really use to evaluate, as one can easily consider them a mix of Natufian (pre-Levant-N), CHG (approx. pre-Iran-N) and WHG. So they should also be very drifted unless there is one population that is missing somewhere, maybe around the Upper Euphrates, that somehow managed to retain very high genetic diversity at all stages, including a weaker initial founder effect but also sustained population levels, no marked endogamy.

      And the region is becoming smaller and smaller, what is in contradiction with this very idea of high population levels and so on.

      Perplexing, really. But the most perplexing of all is that CHG had a sharp founder effect, almost as marked as that of WHG and yet they seem much closer to outgroups.

      For me the provisional conclusion is that there is a good chance that they were more open to interactions with East Asia (low Fst to Han) and other populations (low Fst to Yoruba, not necessarily representing Africans).

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    12. Yes, the different classes of ROH categories would seem to suggest Satsurblia had more recent bottlenecking of ancestors at a more proximate time to the sample than Kotias did (more ROH in long categories), and slightly lower bottlenecking at an earlier time relative to the sample being collected than Kotias.

      Satsurblia (13,300 years old) is the older sample than Kotias (9,700 years old), so the scenario implied may be that Satsurblia is closer to a bottleneck, and Kotias is from a descendant population that is freed from the constraint of a bottleneck itself, so less long ROH, more short ROH, as the long ROH are broken down into shorter segments.


      (Though, note - Ust Ishim sample - http://i.imgur.com/h45dSgG.png also has high short ROH compared to recent Eurasians (though not long), so higher short ROH may have been normative for most ancient populations?).

      CHG is sort of intermediate in overall ROH and intermediate in fst to Yoruba (though more to Levant_N than WHG by far), so I can reconcile both of those that with an intermediate bottleneck and drift, though I think the closeness to Han relative to Yoruba at least probably has some relationship with gene flow to/from East Eurasian groups

      Some indications to me that population exchange with East Eurasians this is likely for CHG and Iran_Neolithic:

      1. In the paper, EHG is statistically shifted to ENA relative to WHG.

      2. All late upper paleolithic and Mesolithic Euro HG seem shifted to ENA relative to early upper Paleolithic Euro HG.

      3. D stats to compare affinity of East Eurasians to Iran_Neolithic and Levant_Neolithic

      D( Mbuti.DG Munda Iran_Neolithic Levant_Neolithic): -0.0185, Z: -4.66
      D( Mbuti.DG Papuan Iran_Neolithic Levant_Neolithic): -0.0159, Z: -3.693
      D( Mbuti.DG Ami Iran_Neolithic Levant_Neolithic): -0.0134, Z: -3.216

      Statistically significant, Iran_Neolithic closer to East Eurasians than Levant_Neolithic.

      D (Mbuti.DG Munda Iran_Neolithic Kotias): 0.0081, Z: 1.827

      Beneath statistical significance, but Kotias closer to Munda than Iran_Neolithic is (other ENA groups follow this pattern).

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    13. Your example of Ust Ishim is not really comparable because he was so much older than anyone else, including us, that his ROH counts represent timelines at best only represented in the shortest segments of the Epipaleolithic samples. I'd expect Ust Ishim to be at the very founding bottleneck of the Epipaleolithic samples if anything.

      It's not in any case a "common trait" of a time: those are, generally speaking, our ancestors: we carry those "scars" too unless they have been shredded so thin we cannot recognize them anymore.

      And that's the question I can't find an answer for: what time scales do the various ROH length categories represent approximately? We know that long ROH segments represent very recent events such as historical inbreeding, but what about short ones?

      I suspect that in your initially linked graph (this one) would better understood if the Neolithic ones would be slided to the right one position (remove the moderns, Satsurbilia should be moved to the left but not sure how much) in order to approximate an invariant chronology. If so, the slopes are much more similar.

      We still have an issue of founder effect bottleneck, which is very generalized among pre-Neolithics (and is probably hidden, not absent among Neolithics) and that might represent either the LGM or the West Eurasian founder effect c. 50 Ka BP (no idea of what timescale the ROH categories can represent in fact).

      In any case the features must be considered as representing a chronology of events that, once adjusted, should be invariant for all, even if each had a somewhat different history. Ust Ishim is just not comparable: any modern is much closer in time to the early Holocene period we are considering here.

      ...

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    14. ...

      Same thing re. "ENA" (i.e. Ma1): he's not as old as Ust Ishim but is still farther from Early Holocene humans than we are. MA1 is very interesting to track the earliest origins of Native Americans when they were still in Asia, in almost perfect convergence with archaeology and haploid genetics (Y-DNA Q, mtDNA X), but it's almost meaningless otherwise. Afontova Gora should be a better proxy than Ma1 because he lived 7000 years closer to us. Still quite old but at least he is barely post-LGM.

      ENA should not produce an effect similar to "Basal Eurasian" in any case but, if anything, the opposite -- closer to root mainline Eurasians because they are old and at least partly external to West Eurasia in the narrow sense, even if related: the westward migration towards West Eurasia c. 50 Ka BP, surely diverged in southern Central Asia (Afghanistan-Uzbekistan-Balochistan) with one branch heading north to forge the basics of ENA and primary proto-NAs and another heading West to forge West Eurasians proper. It's probably true that that Ma1, etc. were affected by a secondary Gravettian wave from Eastern Europe, what muddies things a lot, so rather than Ma1 I'd try to extract a ghost or zombie from Native Americans (Karitiana for instance, as they are very pure) minus East Asian genetics in them. That would give a better "ENA" reference IMO.

      ...

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    15. ...

      Statistically significant, Iran_Neolithic closer to East Eurasians than Levant_Neolithic.

      Could you do that comparing Levant-N and Natufian. I suspect that the exogenous component in Levant-N is similar to Iran-N and hence drifted also to Oriental populations.

      Another question I have but that I don't think can be solved until ancient Indian genomes are sequenced is whether this "orientalizing" deviation responds to East Asian or actually Indian admixture. Munda are actually mostly ASI, which seems to be that Indian aboriginal thing and the score is higher, so no sure how to interpret the affinities to them.

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  3. Karitiana are very drifted, yes, and they serve as an example of how much drift alone can elevate absolute fst.

    In case of BedouinA f3 mixture tests and so on show SSA. For Natufians it doesn't need to be Yoruba per say, but could be something that has more affinity to Africans than to Eurasians. If Natufians' fst was elevated by something with no affinity to Han and Yoruba relative to European Neolithic and Iran Neolithic (which are very different from each other but have the same relative position re: Han and Yoruba) their relative position should not shift towards Yoruba.

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  4. @ Maju
    “Or why not to be ancestral to Volga R1b? After all East European ancient samples (Steppe-gibberish ones) all have strong "Iran-N" component. What is clear is that R1b expanded from West Asia in several directions and that we haven't found it was in Europe before Neolithic. However we haven't found it in West Asia either, not yet, so all options are open”.

    Let's speak again after that Tyrrhenian Italy is tested. No one, except me, thought that R1b1a would have been found in Italy (Villabruna 14000 years ago, WHG, very likely the tribe ancestress of all the R1b1-L389+ in Europe, not counting R-V88 oldest in Sardinia/Italy and not found elsewhere).
    I am waiting that also R1a-M420* is found near Villabruna.

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  5. @Gioiello,
    Isn't it R1b1 too close to originals to mean anything being found in Italy Villabruna? probably R1b1 is close to 18,000 years old, so it can be found anywhere, right. Its not like R1b was hiding under a rock for so many thousands years, upon thousands of years.

    Wasn't it the one found in Kura-araxes P25? so a close call to P297 therefore a step away from M269?

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    1. Evidently it does not automatically mean it's ancestral to modern European R1b (or most of it) but it means that those who denied its presence in Europe prior to Neolithic were very wrong. Same as with mtDNA H.

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    2. Yes, Makes sense. something that is 20,000 years old and still exists must have been around the globe quite a bit. :) - Same for all other haplogroups. I imagine that if we could sample enough we would find this old clades everywhere...

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  6. @Kristiina,
    Regarding your last paragraph, and the fluctuations of EHG here is my alternate story....

    By 7,000 BC a population arrive in southern Caucasus with EHG and mixed with CHG.
    By 5000 BC the Ubaid changes admix all of them, giving the levant and EHG component to Iran_C, to Anatolia_C , Armenia_C; etc
    By 4000/3500 BC they (south Caucasus) had crossed (already with L23) to north Caucasus and giving the Levant component to Steppe and reducing the EHG in the steppe.

    See it’s a matter of time. And also It was south Caucasus moving into steppe (mostly) and not the other way around..

    Just how I see it.

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  7. "Genetic influence from East Asia or a related population is also apparent in all Northeastern populations but even more so in Iran Neolithic. Why?"

    There are sundadont remains in Neolithic Mehrgarh. So perhaps that is the vector.

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  8. Anatolia Neolithic can't be modeled well as a mixture of older genomes. It is not a mixture of Natufian, Iran Neolithic, and "WHG". It might have mixture from people similar to those three but it can't be fully explained as a mixture of them.

    Instead actually Levant Neolithic looks like a mixture of Natufian and Anatolia Neolithic. Also, Iran_Chalcolithic and Armenia Chacolithic look like they have Anatolia Neolithic ancestry. So Anatolia_Neolithic definitely has ancestry or is fully descended from an unsampled Paleo population that affected all those regions.

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    Replies
    1. Sounds interesting, Samuel. What brings you to think that (Northwestern) Anatolia Neolithic is not a mixture of said "founder populations"?

      I'd like if you could explain your proposals appealing to some data, be it from the paper or elsewhere.

      There were many early Neolithic cultures in the area but most can be considered either part of the PPNB complex or of two main Zagros cultures, one of which is probably closely related to the Iran-N sample. See this map, of better even it's source.

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    2. @Maju,
      "Sounds interesting, Samuel. What brings you to think that (Northwestern) Anatolia Neolithic is not a mixture of said "founder populations"? "

      In Supp. Table S8 Anatolia_N is modeled as a mixture of Iran_N, Levant_N, and WHG but the result has high standard errors. Therefore those older genomes can't explain the genetic makeup of Anatolia_N well. This doesn't mean Anatolia_N doesn't have ancestry from each group, it means those genomes aren't perfect or even good references for Anatolia_N's ancestors.

      "There were many early Neolithic cultures in the area but most can be considered either part of the PPNB complex or of two main Zagros cultures, one of which is probably closely related to the Iran-N sample. See this map, of better even it's source."

      That's interesting and could mean Anatolia_N had ancestry from each group. Levant_N has a lot of affinity to Anatolia_N but it looks more likely that Levant_N has Anatolian_N-like ancestry than Anatolia_N has Levant_N-like ancestry(Supp. Table S7.5), meaning Anatolia_N could be descended of Anatolian hunter gatherers who affected the Levant.

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    3. Fair enough. We just don't know enough.

      One thing however to keep in mind is that West Anatolia has not produced yet, in spite of surveys, any pre-Neolithic remains, be them artifacts or people. So my curiosity is more focused on the Neolithic of Syria and Kurdistan, and to lesser extent that of South Anatolia and Cyprus, which seem derived but might have some specifics of their own, because there was some Epipaleolithic in those areas, and some of the ancestry plausibly survived Neolithization.

      However I don't think they could have affected Early Neolithic Levant. If anything we should look in Syria and Kurdistan (Göbekli Tepe and what not).

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    4. My concern with some of the related studies, is that the sampling for
      "Neolithic Anatolian" is restricted to samples from the far west of Turkey; at one extreme of an interaction zone that stretched eastwards to it's polar end in Iran. In contrast to some assertians, the data does not support that West Anatolians were a unique ancesteral source (as is more clearly the case with Iran Neolithics, WHG, EGH, or Levantine). Instead, the westward Anatolian samples, can easily be described as some proportion of WHG to Levantine, and smaller though significant amounts of Iran Neolithic. However, by the contrasting PCA positions of later populations; Chalolithic Anatolians and modern Europeans, who are clearly on a vector between WHG and Iran Neolithic, versus the earliest European farmers, one is forced into imagining scenarios which, ultimately, involve a considerable amount of genetic input from the Iranian plateau. This occurred not mainly through single migratory events into Europe, but through reciprocal gene flow, between early and later neolithic communities which spanned between Turkey and Iran. Of course, later bronze age migrations from the Western Steppe, account for some of this Iranian influence, as well.

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    5. I also had that concern but since August I don't anymore, as Kilinç et al. sampled Southern ("Central") Anatolians, well done! Their paper was discussed here: http://forwhattheywereweare.blogspot.com/2016/08/i-know-i-know-im-decaying-into-total.html

      Their position is slightly clinal but immediate to that of West Anatolian ancient farmers. They may be a bit more northerly leaning relative to what we have seen before, maybe displacing the West Asian reference towards Lebanon but only one sample really seems to tend towards modern Turks and Iranians.

      So IMO the data fits, except for modern pops. being more "displaced" towards the North in terms genetic. Is that all EHG/Yamna/Siberoid stuff? Or is it a problem of "projecting" ancients on modern PCAs? Or was it already present in ancient times at other less obvious localities? Or a bit of all?

      It would have been nice if the South Anatolian samples would have been used here, but guess that research-publication timelines (it's academic ritual that papers must gather dust on reviewers' desks for some six months, plus other bureaucracy related to publication, etc.) don't allow for that. In 2017 maybe? The genomes are publicly available, AFAIK, so anyone with the skills can compare them.

      But what is clear by comparing both PCAs is that there is a direct genetic relation between South ("Central") Anatolian early farmers and Western Anatolian ones, that both Anatolian ancient groups are drifted "towards Europe" (to WHG or the Sardinian modern reference) relative to Iran and Levant Neolithic samples, and also quite close to each other.

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    7. Thanks. Judging from that PCA, the Tepecik samples from South Central Turkey, do appear to be more leaning toward the Caucauses and Iran, which is still in line with the idea that there was reciprocal gene flow between Anatolian and Iranian Neolithics. And there is still plenty of ancient DNA geographically East, which which has not yet been sampled. Also note the intermediate position of Bronze Age/Iron age samples, with respect to WHG and Caucaus/Iran (EHG/Iran_Neolithic), most of which are in close proximity to the position of modern-day North and Western Europeans. This is suggestive of the possibility that Bronze Age populations emerged as the dominant type in Europe.

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  9. Olympus Mons, what you say could be right in general, but...
    1) When I said that, I was refused because for the levantinists it wasn't true: R1b would have come from Middle East, thus not present in Europe before Neolithic, i.e. before the "colonization" of Europe from the Middle Easterner agriculturalists, and, as also Maju said, this line has been demonstrated false.
    2) I gave also a political-economical explanation about that, indicating who funded and funds those presumed scientific researches and the known firm at the center of that. For that I have a general theory and not sporadic observations. Of course Maju is looking at that from his left side which isn't mine.
    3) But for speaking only from a scientific point of view, one thing is having found an R1b1a (pre-P297) 14000 years ago in Villabruna, in what I am saying from at least ten years was the "Italian Refugium", and another thing is having found an R1b1, perhaps also L389+, in Kura Araxes of pretty 10000 years later, when I have explained from so long that Caucasus has only one cluster of R1b1-L389+, that with YCAII=21-23, whereas Italy has at least three (18-22, 18-23, 23-23), and the subclades have YCAII=19-23, derived friom the Italian/Western European samples and not from the Caucasian ones.
    4) The rest is in the more than 10000 letters I wrote.

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    1. @Gioiello
      Well,
      I disagreed with you… in the beginning … now I am having doubts.
      – This is why:
      No secret I believe R1b-M269 is from southern Caucasus Shulaveri-Shomu (7th-6th millennia BCE), and that is where M269 was born and … ok,
      However I always assume that those R1b came from the steppe with EHG and only then mixed with local population that had EEF (or Anatolia_N) and Local CHG and also Iran_N.

      However who is to say that the exogenous population that got there, by end 8th millennia bc, (land of that Kura Araxes r1b P25/M415 in lazaridis paper) actually came from the steppe and not eastern anatolia? At least their cattle and sheep did!
      So an Italian refuge and then moving to eastern Anatolia and then to South Caucasus and them over the mountains to steppe… why not? The time fits.

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    2. Yeah, your Shulaveru-Shomu hypothesis is rather weakened by the results, which provide data points for most of the Armenian paleo-historical periods, without providing any hint that could support your scheme. Sorry.

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    3. MAju, What you mean? -There is no datapoints whatsoever for 8th-6th millenia in southern Caucasus. - And that Kura-araxes was R1b (P25), which lived near the Sevan lake in Shulaveri land.
      What we know is that Shulaveri was and exogenous population that arrived in late 8th millenia to the region.
      What we know is that by 5,000 bc all their settlemnts were abandoned, burned and another population greatly replace them in the region. YOu have datapoints for people before them (Kotias) you have population for people after them (Armenia calcolithic) armenia bronze age... but not "them". They were pushed aside.
      Were did they go?

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    4. We do get a reasonably good sequence with CHG → Armenia-Chl → Arm-EBA → Arm-LBA. Autosomally, we see an increase of (primarily) Levant-Neolithic and (secondarily) EHG since the Chalcolithic (or earlier, maybe even Neolithic), a slight increase of CHG in EBA and finally a significant increase of WHG (European originated admixture?) in MLBA.

      It's true that Shulaveri-Shomu (Neolithic) is not in the sequence but the most parsimonious thing is to imagine them as intermediate between the CHG and Armenia-Chl samples, plausibly with increased "Levant-N" component but not yet the extra "EHG" factor. It'd be maybe this extra EHG element, arrived from Northern Caucasus and maybe bringing the Hurro-Urartean element with Trialeti culture, which caused all the burning and destruction, and yet should be mostly continuous with the previous demic layer, who were maybe enslaved or similar by the Chalcolithic conquerors, somewhat connected to the Kurgan phenomenon.

      Re. R1b (P25), I believe you are seeing too much in that datum, which is not in any direct way (again the same as with the Volga R1b) directly related to Western European R1b-S116 and U106, but rather part of the legacy left in West Asia where R1b in general must have originated.

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    5. H Maju,
      No we don’t see that sequence.
      Look, There was a CHG in south Caucasus and then a big black hole (French getting DNA from samples what would you expect) of 2,000 years where an exogenous population arrived and disappeared. Disappeared is the exact word.
      And only then we have samples of a time we see a Population turnover up to Iran, from a western/southwest source (acc to Davidski..) . So they all look equal by 4500 BC. What a massive “nuclear explosion” must have been the Ubaid. What were they! – from that point on, population you see a Armenia_Chl and Armenia_LBA all looks the same as the new Iran_Chl does as well. – So it does not matter Y-dna, because “something” mix them all. – That 2000 years were the Shulaveri. And its even worst. Look to an Hypsometic map of the region and to be truth, those guys were isolated form the south. Shulaveri is North of Kura river, that even has a moutains terrain south of the river, and completely isolated from the north by Caucasus mountains. SO, left alone from south.

      As well as we need to directly sample Mesopotamia, either Ubaid or Uruk. I think that is the key. One of.
      However I see Shulaveri as something like CHG but with more EHG that leaked from the north Caucasus (near Black sea where later you see Maykop). So, no wonder so many people think Bell beaker to Yamnaya. I imagine My Shulaveri as very much like that bar in the pic above for the Steppe_MLBA. Bell beaker a mix of it with Iberia chalcolithic/Bronze age.

      That is because I bet, I bet, when Merimde in delta Egypt be sample it will blow everybody’s mind because they will be just like that Steppe Mlba (sort of).

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    6. Basically you're appealing to the unknown. I find extremely difficult to imagine that the genetic legacy of Shulaveri-Shomu was (a) totally different from everything else we see in the same area and (b) that it left no legacy whatsoever. Yourself have no evidence to back your speculation and then begin ranting about various geographically distant locations that seem to have no obvious relation. You must understand that it is very difficult to swallow, really.

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  10. Olympus, I do not have much of a theory here. I am mostly observing.

    I am curious to know if your idea is that R1b-L278 (mostly EHG) came from the Steppe to Southern Caucasus 7000 BC and gave rise to R1b-269 and the proto-IE language? Maybe you are not making any presumptions on language, but I would however be interested to know your linguistic suggestions for Ubaid. Personally, I am not convinced that proto-IE originated in southern Caucasus, but the origin of R1b-269 there is not impossible, if we presume that R1b-V88, Villabruna and M73 are separate developments.

    However, after Villabruna, as long as we do not have any contrary evidence, an Eastern Mediterranean origin is even more plausible for R1b. Of course, everything depends on what will be discovered in the future. Maybe your idea will be proven right, maybe not.

    Among other things, the origin of yDNA J, in particular J2b, and mtDNA H is still puzzling me.

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    1. With Eastern Mediterranean I meant European Eastern Mediterranean, in particular the Balkans and also Italy.

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    2. Kristiina, of course I have taken into account from the beginning that the "Italian Refugium" could be also a "Balkan Refugium" and that people migrated to and from these two places, but I opted for Italy for many reasons:
      1) Italy is warmer and Balkans are colder, and in Italy above all the Tyrrhenian part. During the Villanova age (14000 years ago) better Italy than the Balkans.
      2) No doubt that R-V88 and R-M335 was in Italy and not in the Balkans.
      3) For following the discourse above about R-L389+, so far only 1 sample in the Balkans (Diamantikos) and with the YCAII=18-22 found in DeMao and Toniolo (I found, I posted) who is from Veneto and Greece is plenty of Venetian Y, above all R-U152 but very likely also this R-L389+, and perhaps isn't by chance that Cruciani found 5 R-L389+ and 3 were in Italy.
      4) We are waiting that things become clearer in the trees of smal (Sergey Malyshev) I contributed to construct before my banishment from Anthrogenica, but I belong to the race of Catullus: at tu, Catulle, destinatus obdura.

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    3. Of course Villabruna and not Villanova.

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    4. Kristiina,
      I always assumed that the population that arrived in southern Caucasus by end 8th millennia was from the steppe, because of the all R1b from steppe talk, oldest clade, etc etc. – I have recently started to be confused. On one hand there are some (some, not all clear) similarities with some settlements near Zarcos mountains in Iran which made me believe, ok, from steppe, to Iran to southern Caucasus full of EHG. -- On the other hand, latest papers show that they (Shulaveri), or cattle did, arrived with cattle and goats from West…that means Anatolia or Siria…. So I accept both these days. - And biggest variance of R1b, according to papers, are in eastern Anatolia and also a small pocket in the Land of Shulaveri (near sevan lake… where that R1b-P25 was now found).

      PIE ? – Well, earliest pie actually asserted is Hittite, right? A population that moved from East to settle in that Hittite fatherland, hattusas or Nesa.
      Ubaid is also confusing. That L1a found just in the start of the transition after Shulaveri as per laziridis, has made me start to wonder about who actually started the all Ubaid mess. Kura-araxes was a lot of different people, raiding villages that fight a lot. So different bunch of people. And some were probably L1a coming from Iran or even eastwards.
      So Ubaid language… humm I think it was Dravidean. PIE is still intriguing to me. But Shulaveri/r1b (my Shulaveri as I called because I can be wrong) might actually speak PIE… from Anatolia (where they could be from) and latter when they got kicked out and crossed the Caucasus mountains and became part of the steppe (giving them the CHG and Levant collars) also took the pie north. All this happened a thousand years before Yamnaya… so, long time of people crossing to north caucasus. Hell sample Nalchik and lets see, sample Shulaveri and lets see. They manage to sample Cattle and Goats in there… but not inhumations?! Strange.

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    5. And Kristiina,
      Vacation are coming. so if you have the time, while at the beach and want to read a very interesting story that if right will make yuor head into a spin, then my thesis is here... :)http://blogs.sapo.pt/cloud/file/eb6b52b82097d41dfa0e5797a2fa7945/olympusmons/2016/From%20Shulaveri%20to%20Bell%20beaker.pdf

      Actually, latest comment on eurogenes, from a guy called ryukendo kendow which is running stats is (at made my heart race)...

      "Nevertheless, in contrast to the previous work having Bell Beaker as a simple two way mix of Central Europeans and Steppe peoples, which led some people to suggest a simple movement from Central Europe to Western Europe, this analysis seems to suggest that there was a movement from Iberia, (specifically Iberia and not other places due to the slight African ancestry in Iberians distinguishing them from other Neolithics,) combined with a movement from the Steppe and the Balkans with some Middle Eastern ancestry, creating a mixed superstrate in the Bell Beaker. Or perhaps the movement was due to elite circulation in a network stretching from Iberia to a balkanised and steppe-ised Central Europe, thus allowing the two populations to merge in the elite members. I think the old two-way mixtures were limited by a constrained choice of source populations, and a failure to appreciate how complex the situation could possibly be.."

      Read my thesis... and all is explained.

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    6. Ryukendo is pretty good and I value his opinion. Also it fits with my understanding so far of the issue, although IMO the Vasco-French area may have played a greater role than acknowledged so far, because of:

      1. Very early "modern" mtDNA pools in Paternabidea and Gurgy.

      2. R1b-S116 seems originated in France, rather towards the south or southwest.

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    7. sorry for asking this here, since it is quite off topic, but after all these years of dna studies performed on ancient human remains, do we finally know if the north african ancestry in Spain that is stronger in the west and weaker in the east is mainly of moorish or prehistoric origin?

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    8. Prehistoric without doubt. The assumption of Muslim Era origins was hastily done in early studies because of, well, cliché: simplest available explanation for imprecise data and, well, geneticists are not prehistorians. Recent studies have acknowledged this issues: the Muslim period alone explains very little because it should have an impact from SW to NE, from Badajoz to Zaragoza and not from Asturias and Cantabria to Western Andalusia.

      However more research surely needs to be done, particularly on ancient DNA and I hope (being sarcastic) that the new governments of Iberia and the Brexited EU, invest more (or at least something!) in archaeogenetics. It can be taken from the king's salary, I guess.

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    9. With respect to steppe ancestry in West Asia, take a look at this map that David posted in 2014 showing the spread of microblade technology from around Lake Baikal:

      https://lh3.googleusercontent.com/-U3ge2hjOsnY/U52wTUExYvI/AAAAAAAAAmg/NIotwSYVLtI/w350-h297-no/The_Emergence_of_Pressure_Blade_Making_Fig_2-15_small.png

      I think that offers a pretty solid vector for the spread of ANE.

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    10. Microblade technologies have been claimed to originate in many places and to this date one of the most plausible origins seems to be India, where blade and microblade tech appearances are synchronous c. 30 Ka BP.

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    11. ... or 35 or 38 Ka. Not sure right now, just not old enough to be at the origin of Western UP (blade) tech but close to.

      What is a "microblade"? A small blade. There's no qualitative jump, just a refinement of blade tech.

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    12. It's 45 Ka old, totally overlapping with the earliest Western UP!!!

      This is the Indian microblade link: http://forwhattheywereweare.blogspot.com/2013/07/indian-microlithic-industry-almost.html

      And the original paper:
      http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.006928

      BUT there is an even older microblade group from South Africa c. 70 Ka BP: http://forwhattheywereweare.blogspot.com/2012/11/advanced-lithic-tech-70000-years-ago-in.html

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    13. I believe this is specifically microblades produced through pressure knapping. 25 Ka according to the source. Here's a more readable version:
      https://drive.google.com/file/d/0B9o3EYTdM8lQb1JScVI1TXpxaTA/edit

      Original source: http://www.springer.com/us/book/9781461420026

      David's original post: http://eurogenes.blogspot.ca/2014/01/another-look-at-lazaridis-et-al-ancient.html

      I think ANE likely had a great deal of ancestry from India though for what it's worth. Haplogroups Q and P almost certainly came that way.

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    14. "Pressure knapping was invented in different locations and at different points in time"...

      In fact, I think it was first invented in some variants of African MSA (see this) and later also in the Solutrean (that's how they made such beautiful blades) and probably also in American Clovis culture (comparable to Solutrean although unrelated for all we know), and probably also in the Indian techno-culture mentioned before.

      Even leading to Neolithic, as the book seems to point to, there's at least another source AFAIK in the Nile area, which would be the core Afroasiatic (or maybe Eastern Sudanic plus Afroasiatic) group, that decisively influenced the Levant and NW Africa in the Mesolithic.

      It's interesting indeed to know that there may be yet another source of the same kind of technique but I would not consider it the only one, really.

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    15. Also the core area represented in that map includes North China, with arrows leading to Japan and, of particular interest, to NE Europe, in which must be related to the expansion of proto-Uralics (who are not too good for ANE reference and do instead look East Asian admixed). These proto-Uralics, as I believe Kristiina has mentioned some time ago, also brought pottery from China, although it remains unclear or even unlikely that it was at the origin of Western pottery (although who knows!)

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  11. Genetiker says that the R1b from Kura-Araxes is an R1b1a1b positive for V1956 (Y: 8430895 G>A)
    Sample ID HG 8430895
    REFSEQ G

    Also the sample from 1KGP from Puero Rico is positive for V1956 and all the subclades from R-P297 are neagtive
    HG00640 R-L389* A
    HG00640 20120522 PUR R-L389*
    L388/PF6468 • L389/PF6531 B2b

    The sample from Puerto Rico is very likely of the Iberian R-L389 haplotypes and all the other known R-L389 which are most diffused and with the highest variance in Italy, thus the Caucasian sample from Kura-Araxes, as I am saying from so long, belongs very likely to the Caucasian R-L389 with YCAII=23-23 which is presupposed derived through a RecLOH from the basal 18-22 and 18-23 diffused in Italy, which are a sister clade of the R-L389 ancestor of R-P297. But the Villabruna sample of 14000 years ago has two certain mutations at the P297 level, thus it is more likely of the family which brought to the R-P297* and subclades. Anyhow no doubt that my theory of an “Italian Refugium” adds another proof. Let's go on.

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  12. Maju

    What You know about Y dna of Subartu Hayasa and Urartu? I suppose not much otherwise You wouldn't lump three different things into the same basket.
    As for Armenians and Phrygian. You can't cite any recent genetic paper suggesting such a thing. Please read Brittanica and find any mention of Balkans. So please update Your theories about Armenian ethnogenesis.

    https://www.britannica.com/topic/Armenian-language

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    1. I'm not mostly mentioning Y-DNA here, because it's just one side of the evidence, and for aDNA the most interesting stuff is usually in the autosomal DNA and mtDNA (not enough Y-DNA save rare cases to be sure which was the pool, it's getting better but still not enough). Also I dislike patriarchal obsession with Y-DNA, when it's obviously just another piece of the puzzle.

      Anyway, just as we don't have yet aDNA for Shulaveri-Shomu, we don't for Urartu. The exact scope of Subartu is unclear, although it may refer in general to Hurrians, but if the Hurrian lands included Armenia, then we do have one or two samples here, as both belong to the Bronze Age. As for Hayasa, I'm not sure what it is right now.

      "Please read Brittanica"...

      Why should I? It's a commercial resource and therefore for posh wannabe-bourgeois people, not me. Anyhow, I doubt that an encyclopedia is any better than up-to-date genetic and archaeological knowledge: encyclopedias are fine when you know nothing on a subject and need a starting point, references, etc. but they are often not enough.

      The Armenian language seems most related to European IE languages, particularly Greek, what fits well with the Balcan (Bryges/Phrygian) theory, also supported by ancient claims by historians (Herodotus?), by the fact that Hurro-Urartean is clearly not Armenian nor IE (so not Iranian nor Anatolian either) but most likely related to NE Caucasian languages like Chechen (and IMO, with due caution, also to Sumerian maybe), by the fact that to West Asian R1b lineages, Armenians (and to lesser extent Antolian Turks) carry Europe-derived terminal R1b lineages, what is what causes the confusion about "high diversity", which is just raw diversity, not the really relevant basal diversity. There was a paper in the last years on that issue but I can't find it right now.

      I think it's you who must understand that Armenians are Iron Age "phrygianized" Urarteans (Hurrians). The Urartean roots we can track in the data posted here: i.e. a Neolithic mix with some evolution upon the arrival of the Kura-Araxes culture from the North.

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    2. This comment has been removed by the author.

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    3. This comment has been removed by a blog administrator.

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    4. Nothing has happened since you were banned that has changed your status, Onur: you are still banned, hence whatever you say, right or wrong, will be deleted and ignored.

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  13. I know you hate talking about this subject, but what is the implications of this study on the subject of the Origins of Ashkenazim Jews and modern day Palestinians relative to the original Levant population.

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    1. I don't hate to talk about that at all, I made some lesser self research on the matter in 2012 that seemed to confirm the camouflaged but unavoidable conclusions of Behar and Atzmon two years earliers: Palestinians are in essence "the real Jews", Jews appear to be converts from other ethnic backgrounds (from further North in the case of Roman Jews, maybe Anatolia or Cyprus).

      See: http://forwhattheywereweare.blogspot.com/2012/01/spehardi-jews-in-context-of-levant-and.html

      Now, what does THIS say about the matter? Well, I'm not sure, it probably just redefines the components but not the essence of the problem, because the affected populations are the same and subject to the same problems like biased one-sided Zionist hegemony of research and what not.

      Ideally we'd know by now what is the genetic composition of ancient Jews and would compare with modern populations directly and without bias but, while the current colonial and genocidal situation remains, that seems most unlikely to happen. Because it is a clear case in which science affects politics (propaganda, ideology) and results in either direction would support or erode either side's claims, particularly the extremely weak zionist one, based only on old mythological stuff (the Bible) and very creative (but certainly false) reinventions of Medieval History.

      Basically today you can dig Ancient Judea's graves and get the DNA of the contemporaries of Jesus and even David and get them sequenced. But doing that is political and the Zionist entity will exert absolute control. Maybe in Jordan with Irano-Russian funding? Because the West is not going to invest in anything that upsets the Zionist discourse and that's why after Atzmon's and Behar's 2010 papers nothing more has been published on Jewish origins: the truth was becoming too apparent and uncomfortable to the Zionist ideology.

      It is a case in which the historical truth, archaeogenetic in this case, may and will surely erode dramatically the claims that some political projects have staked way too assertively, a bit like with Hitler's non-existent "Aryan race" - but with ongoing political implications. Hitler would have hindered any research that could prove his racist theories wrong, similarly, the Christian-Zionists (more numerous and powerful than the Jewish-Zionists) who control NATO won't be happy about finding that maybe modern Palestinians are approximately the same as ancient Jews, while modern Jews are something else: converts from other areas.

      But nothing I can see in this paper affecting it.

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    2. On second thought, this paper actually seems to support my stand in favor Palestinian local roots and against the (totally made up) myths and legends of Zionism, which claim without any support that Arab invasions radically changed the landscape. Why? Because what we see is that Bronze Age Canaanites were pretty much like today Palestinians and not tending towards the North (Turkey), as Roman Jews (Sephardi, Ashkenazi, etc.) do.

      So yeah, it has implications: even if the modern populations are not labeled, any trained eye can identify them by comparison with other similar PCA graphs, like the one in this new entry, which is labeled.

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    3. Thank you for the insight.

      I also see in the plot included in the study that the Natufians cluster around Bedouins and Palestinians and slightly to Saudis.

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    4. Yeah but it's less clear because those, much like Neolithic Levant, are an almost "primeval" population and it would be nice to confirm their similitude or difference via other analyses (PCAs can play many visual tricks, they can be too simple and can place isolates where they do not belong at all). That's also true for Bronze Age Levant but those are clearly a much more modern-like population, so I have no reasonable doubt with them.

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    5. I was above asking for a contemporary of David, well Bronze Age Levant are close enough (rather contemporary of Moses but good enough). Iron Age and Roman Era data points would be cool to have anyhow, for further confirmation, because both the Jewish invasion of Canaan first and the brutal Roman repression of the Jewish revolts later may have altered the genetic landscape somewhat, because the written references do hint of possible partial genocides at those two episodes, something that definitely did not happen with the Muslim invasion, quite well documented.

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    6. Another interesting data to have would be a regionalized modern Palestinian dataset with pre-Naqba geography, because we do know that Palestinians show important internal diversity and some clinality but we don't know it would plot on a 1946 map (Bedouins excepted because they are treated separately in all cases).

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  14. The greater discontinuity might actually be Early Bronze <-> Middle/Late Bronze, rather than Middle/Late Bronze <-> Iron. I think archaeologists usually refrain from calling the population of the Early Bronze Age "Canaanite".

    re: your last comment — any particular insights you have into Palestinian regional (or religious) differences, even across poorly-labeled datasets? I've never seen any good treatment of this topic.

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    1. "The greater discontinuity might actually be Early Bronze <-> Middle/Late Bronze"...

      Which is the evidence for this claim if any? I'm amiss.

      "I think archaeologists usually refrain from calling the population of the Early Bronze Age "Canaanite"".

      That's optional/arguable I guess but the fact is that the Semitic invasions happened c. 4000 BCE, much earlier than the period you're discussing. And it is generally accepted, I understand, that Western Semitic (including Hebrew, Phoenician, Aramean, etc.) originated at that time. Correct me if I'm wrong, please, because I have no time to double-check my claims right now.

      "any particular insights you have into Palestinian regional (or religious) differences, even across poorly-labeled datasets?"

      I don't have any. Just that in Behar's limited (too global) ADMIXTURE analysis they show two components and a clinality among them. In my own analysis (see link in previous comment above) they appear to have many more components but I did not produce an individualized analysis (don't know how to) and therefore I only suspect that it may have some clinality. Some of those components are almost exclusive to Palestinians, so, if they can be confirmed by more elaborate or complete analyses, they may indicate several original population clusters. My own hunch is that Galilee and Judea should be two distinct centers but greater complexity cannot be excluded (for example: coast-Jerusalem-Jericho, IDK).

      "I've never seen any good treatment of this topic."

      Me neither but the generic samples are in the public domain and so is the software (algorithms) to be used such as ADMIXTURE. It just requires some genuine interest and a half decent computer with Linux (R and ADMIXTURE do not run on Windows AFAIK). Naturally regionalized samples would be of great interest but they don't exist because nobody has ever bothered obtaining them. I truly hope this changes, not just because of justice but also because the high genetic diversity of Palestinians (the highest out of Africa per some old study) is of interest in itself, more so being a region of almost continuous human habitation since many millennia ago.

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  15. So where exactly so Arabians like Saudis and Yemenis fit into all of this? Not to mention North Africans like Egyptians and Berbers (especially Berbers)? Are Arabian descendent of the Levant farmers or something else?

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    1. It is a very wide question, Prince, very briefly and always in my best and quite approximative understanding (for further resolution, use the open source algorithms and open access genomes yourself in optimally designed analyses):

      1. Arabia:

      Typical Peninsular Arabs seem to be in essence Neolithic settlers from ancient Palestine, a branch of the Levant-Neolithic sample above, with some further admixture but less than Bronze Age and Modern Palestinians probably.

      However there is some "other stuff" that has not been properly researched and that may well be the so much fabled "Basal Eurasian" thingy or its cousin. For example there's a lot of African-derived mtDNA but in many cases it seems very old (totally NOT medieval-modern trade routes, slave trade and such), maybe from the migration out of Africa or maybe LSA-related backflow. See this entry in my old blog.

      I suspect I have spotted an autosomal "Basal Eurasian" component in Saudis and one but not the other Lower Egypt samples, but nobody else has bothered replicating or improving my analysis, or even proving it wrong, so unsure. See this attempt to analyze Egyptians (before realizing that both Egyptian samples are from the Delta and none from Upper Egypt or Nubia).

      Some probably very interesting "fossil" populations like Mahris and Socotrans have not or almost not been researched (on Socotrans there's some data on their Y-DNA but nothing more that I know of, on Mahris nothing at all). Yemenis themselves seem to partly belong to this category of ancient populations, with more African-like constituents than common in the peninsula that (I insist) may be very old in many cases, not at all recent.

      ...

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    2. 2. North Africa: I have already discussed them in previous comments but I'll review here the main references and my onion-like layered reconstruction of their make-up.

      2.1. The oldest layer could well be from Aterian times, i.e. equivalent to Out-of-Africa elsewhere. Tentatively detected as mtDNA (L3 and L2 specific subclades, see relevant link in point #1) and as distinct autosomal component (concentrated in South Morocco, which may have acted as refuge) that appears to be as distant from everything else as everything else is from each other (i.e. "racial" or "continental" level of separation).

      2.2. A European layer from the Solutrean-Oranian (aka Iberomaurusian) interaction. This is clear in about 40% of the local mtDNA (H1, H3, H4 and H7, and maybe also their cousin V). Even U6 has been recently suggested to be of European origin after a Paleolithic Romanian was found to have it and the rare U6c was detected in Spain, making both Morocco and Spain equally good candidates for the origin of the lineage as we know it (elsewhere in Europe it was erased by the Ice Age bottlenecks). Archaeologically speaking, the Oranian/Iberomaurusian is the first known Upper Paleolithic of North West Africa (West of Cyrenaica, where probably Asian-derived Dabban industries are older). So the European origin story of this layer is quite solid IMO.

      In addition to mtDNA, we see how the Guanche (ancient Canarian) mummies carry some European Y-DNA, both I and R1b, which are rare (R1b) or almost absent (I) in today's North West Africa. These "European" male lineages were probably more common in the past but direct evidence (ancient DNA) is lacking so far.

      2.x. There is a big question mark on Y-DNA E1b-M81: its ultimate origins are necessarily in the Middle Nile Basin (pre-partition Sudan approx.), like all other E1b, but the lineage is distinct enough for us to be uncertain on when exactly (and how) it arrived to NW Africa, from where it spread to parts of Europe (particularly West Iberia).

      2.3. The Capsian (or Afroasiatic or proto-Berber) layer, which archaeologically is clearly from c. 10 Ka BP and centered in historical Inner Numidia. This time frame is also good for linguistic reconstructions of the Afroasiatic family. It probably originated in the area of Nubia and brought with it lineages like Y-DNA E1b-M78 and J1, and also mtDNA ones and autosomal elements of NE African (Sudan or Horn-like) affinity but also maybe Arab-like ones.

      2.4. More uncertain but indeed possible is that some further layers of NW African and Arab (South West Asian) affinity arrived with Neolithic. We just don't know enough about this phase, although it's often considered a local evolution of Capsian, so the impact should not be massive.

      2.5. Semitic influxes: first the Phoenician one, later the Arab-Muslim one. The main marker of these historical inflows should be Y-DNA J2, which is clearly a newcomer and found at variable frequencies in all modern West Asian populations.

      For autosomal data see:
      → http://forwhattheywereweare.blogspot.com/2011/12/north-african-genetics-through-prism-of.html
      → http://forwhattheywereweare.blogspot.com/2012/01/north-african-autosomal-genetics-again.html

      The former is my own exercise and the latter one, a bit more professional, by Brenna Henn (one of the most dedicated researchers of African genetics). They are strikingly similar in the strategy and results, however as I went deeper in the search of components, I found (?) a possible Aterian component that Dr. Henn did not spot.

      Hope this helps.

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    3. PS- A couple of references of interest for NW Africa:

      On mtDNA H, including at least two major studies on NW African H:
      → http://leherensuge.blogspot.com/2009/04/brief-review-of-recent-mtdna-h-info.html

      The Y-DNA Guanche mummies' survey:
      → http://leherensuge.blogspot.com/2009/08/ancient-guanche-y-dna.html

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    4. *Erratum: I have already discussed them in previous comments

      Actually it was in some other entry, where I had a bountiful debate with Basque-Tunisian Jamel on NW African origins, touching many issues. For some reason it was in this entry (off topic but I don't care if interesting):

      → http://forwhattheywereweare.blogspot.com/2015/09/detailed-analysis-of-ancient-atapuerca.html

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  16. This study labeled as Neolthic Anatolian, is in fact, predominately Iranian. So the study is essentially suggesting, though non-explicitly, it's not just that Iranians moved Northwards into the Steppe, and into India, but also into Europe, through Anatolia. Still I'm a bit confused, another study with remains of single Neolithic woman from Ganj Dareh, in NW Zagros, shows to be quite distinct from Anatolian Neolithic samples from the far West of Turkey, and early farmers of Europe. That was likely the illusion which resulted from using only a single Iranian sample, and excluding Neolithic samples from more Eastern parts of Turkey.

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    1. Where do you get that idea from? Because I'm looking at the PCA above and Neolithic Anatolians (downward red triangles) do not even fall close to modern Iranians but rather to Cypriots, Greeks and even modern Anatolians (although they also are drifted to the bottom, to the "Sardinian" component, logically).

      On the other hand, Neolithic Iranians do appear closer to modern Iranians and particularly to Caucasian populations, what again is quite logical, as they seem to approximate the seed of that Caucasus-Baloch or ANI component we detect in modern populations from Caucasus to India (and also in early IEs from the steppe but not in Neolithic Europeans and their less genetically indoeuropeanized descendants such as Sardinians, Iberians or Basques).

      "That was likely the illusion which resulted from using only a single Iranian sample, and excluding Neolithic samples from more Eastern parts of Turkey".

      In this paper they use 5 or 6 Iranian Neolithic samples, I really don't know what you're talking around. Is this something "found" independently by Davidski? If so, I wouldn't mind a link, so I can check how good is his reasoning.

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  17. In the body of your post, with the image titled "This graphic shows pretty well how the ancient populations of West Eurasia are expressed as a mixture of those four founder populations". The Anatolian_N carries a sizable Iranian_N component, in Red. Am I not interpreting that correctly? It would make sense, because High resolution global PCA's do not suggest modern Iranians and Turks are highly distinct populations. In fact, there position is usually adjacent (though Iranians are more heterogeneous), along with southern Caucus populations. I am suggesting that what they refer to as "European/Anatolian farmers", is essentially a mix of Iran_N + Levant_N + WHG (through backflow). Also, the Steppe had a significant Iranic component, and through bronze age waves, contributed to the later peopling of Europe.

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    1. Yes, I call that color "orange" but otherwise yes.

      I wrote in the entry that Anatolian early farmers seem to be "a mix of both West Asian farmer groups [Iran and Levant], plus a sizable fraction of Western Paleo-european [WHG] ancestry".

      "I am suggesting that what they refer to as "European/Anatolian farmers", is essentially a mix of Iran_N + Levant_N + WHG (through backflow)".

      Yes indeed. That's correct, although the WHG component seems to increase as they migrated West first, and later as time passed, especially in the far west, so they also admixed with Aboriginal Europeans in Europe.

      "Also, the Steppe had a significant Iranic component, and through bronze age waves, contributed to the later peopling of Europe".

      I would not call it "Iranic" because it suggests that they already spoke Iranic languages, what is surely not true, but rather "Iran-Neolithic" or "Caucasus-Baloch" or even "ANI" (Ancient North Indian, a South Asian component of Neolithic West Asian origin almost exclusively). But, semantics apart, I agree.

      I would think that the NE West Asian (Zagros or Iran) Neolithic must be considered a distinct population from that of Levant (PPN-A/B) Neolithic and that each had their own areas of expansion: the former expanded to Iran and India and also to Central Asia and, through the Eastern Caucasus, to the Western Eurasian steppe, where it contributed to the Indoeuropean genesis later on (aprox. 50% Iran Neolithic or similar, 50% EHG). The latter may have had its greatest direct impact in Arabia Peninsula and maybe (to be confirmed) in North Africa. There is, it seems now, a third admixed population in South Anatolia that would seed the mainline European Neolithic.

      More difficult would be to make a linguistic extrapolation but I think we know with reasonable certainty that:

      1. The "Eastern" Neolithic (Iran, India) spoke Elamo-Dravidian.
      2. The "Western" Neolithic (most of Europe, Anatolia) spoke initially Vasconic languages, ancestral to modern Basque and historical Iberian.
      3. The "Northern" Neolithic (Western steppe) spoke Indoeuropean.
      4. The "Southern" Neolithic (at least the arid zones of Arabia and the peripheral Fertile Crescent) spoke Semitic, in turn a derivate of Afroasiatic, probably arrived, from NE Africa, to the Southern Levant in the Mesolithic.
      5. There were other families like Sumerian (also apparently derived from the Zagros Neolithic), Hattic (rel. to NW Caucasian or Circasian?), Hurro-Urartean (rel. to NE Caucasian quite probably), etc.

      The possible links between the various families are difficult to understand but some must have existed, at the very least in "technological" vocabulary like agricultural or cattle terms, urban development words (uri/iri/urbs/uru/ili/uli), etc. My impression is that Basque/Vasconic and Indoeuropean are closest among surviving West Eurasian families, while Dravidian is farther apart, but I don't know why or even if I'm really correct. Others have underlined some vocabulary similitudes between Indoeuropean and Semitic and yet others suspect that Elamo-Dravidian and Indoeuropean are somehow related. The question is open but it's good to understand the archaeological and genetic roots, fundamentally (but not only) Neolithic West Asian ones, that might explain such connections.

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