The genetic structure of the world’s first farmers

The authors don't think Basal Eurasian came from Africa, because Basal Eurasian peaks in Neolithic Iranians.

But while HG's all had Basal, no one was a pure Basal. It clearly is not African - this paper reaffirms that - so how can that be?

It must therefore be something very old and it needs to have happened before the UP. So, Basal remained in ME, admixture with Neanderthals happened in the Caucasus or Anatolia and the latter back migrated. Then diversified.
 
I1707 = T
age = 7722-7541 calBCE (8590±50 BP, Poz-81097)
found = 'Ain Ghazal Jordan
SNP's = 152234
MtDNA = R0a

I1707
: T(xT1a1, T1a2a) (PPNB )
This individual was derived for mutations PF7466, CTS7263, CTS10416
defining haplogroup T. It was ancestral for FGC3945.2 (T1a1) and
P322 (T1a2a). Thus, it could be designated
T(xT1a1, T1a2a). It has been suggested that haplogroup T first began to diversify in the Near
East9
and our results document that it was present there in some of the earliest Neolithic
communities of the Near East, providing a plausible source for its appearance in the Early
Neolithic of central Europe6.


While some Y-chromosomal lineages (such as H2, T, and G2a) span more than one early
Neolithic population in West Eurasia, none of them are found in all of them (Levant, Iran, and
Northwestern Anatolia/Europe), in agreement with the conclusion based on the analysis of
autosomal data that the Neolithic of West Eurasia either began (or was taken up soon after its beginning) by genetically diverse populations.

The Ydna found in and around Karsdorf ....where all G2a, H2 and T .............as per the note above, it means they have been travelling together for many many centuries

T-P322 is mostly found in the Levant , Armenia and Germany

Ancestral = Negative, He doesn't belong to P322.
 
This could be a scenario:

The authors found that I1945 belong to P1-P282 but was negative for R1b1a2-CTS12478. This would mean that R1b1a2-M269 is necessarily discarded? NO!

According to YFULL R1b1a2-M269 have been formed 13600ybp BUT TMRCA for all descendants is only 6400ybp!

Anyone knows when CTS12478 appeared? Because between 6400ybp and 10.000ybp there are 3600 years for accumulate new mutations! What if CTS12478 is younger than the sample?
 
Just finished the Supplement and then took a look at other sites to see the comments. Some were insightful, some very disappointing. Every person whose pet agenda is at all negatively impacted has pulled out the knives. Without being able to point to anything wrong with the analysis, and without having even looked at the actual samples, one blogger stated outright that he's out to disprove the conclusions of the paper. Very sad. Not, of course, that any group of researchers is necessarily correct 100% of the time, but this particular group has a very good track record, and some of them created the very statistical programs being used. So, we shall see.

the "reasonings of this blogger you mean are so pathethic, he doesn't even try to hide his agenda. He always jumps out with a knife when it is about that I1945: P1(xQ, R1b1a2, R1a1a1b1a1b, R1a1a1b1a3a, R1a1a1b2a2a) individual and despite knowing nothing, "Assumes" it must be R2 without any reasonable reasoning and his believers who seem to not be able to think for themselves just swallow it ^^
Especially some of those guys on Anthrogenica are the worst. I haven't seen such a bunch of non thinking individuals on one place for long time. You can't even read their coments properly without account as if they are some kind of special organisation but all I see is that roughly 90% of the freakn Forum are too lazy to think for themselves and eat everything out of the hand of him. He doesn't even need to give a reasoning, He could write "it is so because I said so" and several of these individuals including the Admin would give him just out of their "principles" a thumps up. Remember I got blocked there not because I insulted anyone but because I was one of the few who tackled that "prophetic bloggers" words. They blocked me with the reasoning of creating too much "controversy" lol. So you are only allowed to be in this special group if you swallow what a few individuals spit.

When you ask how is that this individual is going to be "R2" ( chance of 1 to possibly 1/4 at least considering how many R1a and R1b subclades are possible) all you get as answer is a "Haha no R1 in ancient Near Eastern. " while the sample is most likely some branch of R1a or R1b. And take in mind where R2 is there shouldn't be R1 far off either.

By so much pathethic ness I just wish R1 is going to be found somewhere in Africa just to piss them off ^^




Now about the EHG in Calcolthic Iran, I think I did write this under this bloggers comments once, We might even find some EHG on the Iranian Plateau because I believe there has to have been something ANE or even Proto EHG like in South_Central Asia. So I believe this EHG indeed might have come from South_Central Asia.
Another possibility is that this is very ancient relationship between the CHG like and EHG like ancestry.

[QUOT]Eather than accept this formulation, it was stated that the intrusive population to the steppe might be a combination of EHG, CHG and CT or "Old Europe" presumably, and that Lazaridis et al never bother to test that possibility. Well, uh, they did test it, and show the results in the Supplement for a possible admixture of EHG, [/QUOTE]

Yup Lazaridis just doesn't know what he is talking about because he didn't test the possibility of EHG, CHG and CT (sarcasm), everything just don't come too close to a possible Iranian Plateau origin of PIE lol.
 
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This paper includes lots of Middle Eastern hunter gatherers. They all had Basal Eurasian. In Iran and Levant, the later farming population's were the decendants of previous hunter gatherers in Iran and Levant. Basal Eurasian has nothing to do with farming. pre-farming Iranians were had ANE but weren't ANE-rich, at least compared to EHG and Native Americans.



Please Fire_Head read the study, above I directly quoted from the study. The Iranian Plateau farmers are rich in ANE, or have rich ANE like ancestry.

The paper clearly showes Mal'ta (Proxy for ANE) being labeled as ~28% Iranian Mesolithic/Neolithic like, 10% CHG like. So the Authors assume that ANE itself has a huge chunk of Iranian related DNA. This is why Iranian Neolithic doesn't show any ANE admixture. What they believe there is ancestry from the Iranian Plateau in ANE and not vica versa.
 
But while HG's all had Basal, no one was a pure Basal. It clearly is not African - this paper reaffirms that - so how can that be?

It must therefore be something very old and it needs to have happened before the UP. So, Basal remained in ME, admixture with Neanderthals happened in the Caucasus or Anatolia and the latter back migrated. Then diversified.


Yes this ^

Basal Eurasian must have been somewhere where there wasn't much Neanderthal population, let's say somewhere like the coastle area of Iran. While the other non Basal Eurasian, Eurasian people went up into Anatolia, more North of the Iranian Plateau, Caucasus and mixed for the first time with Neanderthals.

Later these Neanderthal mixed people mixed with the Basal Eurasians, and there we have what we call A_Farmer, L_Farmer and I_Farmers, CHG.

The authors even assume that the only difference between Iranian_Farmers and CHG is that the former got effected more by a Basal Eurasian population while the letter less.

And the relationship of Levant Neolithic to Anatolian Neolithic is exactly the same as the relationship of Iranian Neolithic to CHG.

The letter seems to have less Basal Eurasian than the former.

Means Basal Eurasian came and mixed into a WHG like population in the Levant and a ANE like population in the Iranian Plateau.

Now Basal Eurasian could be from anywhere in the coastle Iranian region to Arabia.
 
I've been looking at the modern PCA in the paper. Does anyone know of a site somewhere where it's explained where the modern samples for this data set were collected? I'm interested, for example, in whether those are all mainland Greek samples. I'd also like to know if the "North Italy" samples include Tuscans. It looks like it to me, but I hesitate to say so without knowing more about the data set.

For ease of reference to the PCA with the ancient samples:
2fdrZf8.png


Look at what happened to the Anatolian population from the Neolithic to the Chalcolithic. There's obviously been a lot of gene flow from the Caucasus. I think my brain is overloaded. Is the Anatolian Chalcolithic sample the Kumtepe 6 one just prior to Troy? If so, what some of us saw in the Hofmanova results is correct?

You can definitely see the European samples being dragged over by the WHG admixture over time, but not very much.

I don't know how much weight to put on where they fall versus modern populations. Did anyone notice in the methodology where they described how the projections were done? I just skimmed much of that.
 
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Someone on anthrogenica posted the fst table for Anatolian Neolithic. Interesting, yes?

Lazaridis Neolithic paper-FST (1).PNG



The actual Middle Eastern populations are much more distant. Surprisingly to me, so are the Ashkenazim. That's just more fodder for the political wars, of course, although the difference is small.

The Canary Islanders keep coming up with a high relationship. Their more "exotic" ancestry is too small, I guess, to pull them very far away.

Of course, the absolute winners are the Adygei, Abkhasians, and Albanians.

I've been thinking about the routes of the Neolithic into Europe. Perhaps what we're seeing here is the Cardial route group having relatively more Levant Neolithic because they took off from further north near modern day northern Syria/southeastern Turkey? The group that went due north quite a bit later perhaps had more CHG? (although the paper models them as being part Levant Neolithic) That might explain the slight differences between the Hungarian Neolithic and the Spanish Neolithic?
 
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Seems like the paper does "confirm" another of my theories, namely that before Neolithic (possibly even a little earlier) the Iranian Plateau was populated by a very ANE like population, than this ANE like population mixed with an "incoming" population (Basal Eurasian?) that brought farming to them and is the reason why Iranian Farmers are more Basal Eurasian than CHG which seems to be the "only" difference between both groups.

This same "Basal Eurasian" population seems also to be the one who brought farming to Natufians. Because Natufians are basically Basal Eurasian and something WHG like.

With other words EHG seem to have Iranian mesolithic ancestry minus the Basal Eurasian.


What you say seem logical until a certain point (the Basal Eurasian would have been sent by Neolithic southern farmers?); a point seems less certain to me: the "iranian mesolithic" label for EHG; perhaps are you thinking CHG and not EHG? Could you confirm or infirm it?
 
Someone on anthrogenica posted the fst table for Anatolian Neolithic. Interesting, yes?

View attachment 7812

The actual Middle Eastern populations are much more distant. Surprisingly to me, so are the Ashkenazim. That's just more fodder for the political wars, of course, although the difference is small.

The Canary Islanders keep coming up with a high relationship. Their more "exotic" ancestry is too small, I guess, to pull them very far away.

Of course, the absolute winners are the Adygei, Abkhasians, and Albanians.

I've been thinking about the routes of the Neolithic into Europe. Perhaps what we're seeing here is the Cardial route group having relatively more Levant Neolithic because they took off from further north near modern day northern Syria/southeastern Turkey? The group that went due north quite a bit later perhaps had more CHG? (although the paper models them as being part Levant Neolithic) That might explain the slight differences between the Hungarian Neolithic and the Spanish Neolithic?
Angela, the attachments don't work in both posts.
 
I didn't read that. The paper states:
Got it now, thanks for explaining.

CHG was paleolithic and mesolithic.
Yes, but overlapping with Iranian Neolithic as perf figure 1a.

Any idea why Figure 1c is not in tune with Figure 4b? According to 1c Anatolian N is mixture of mostly Natufian/Levant farmer with WHG. According to 4b mostly Iranian N, then Levant N, and some WHG. 1b PCA chart also plots Anatolian and European farmer between position of Natufians and WHG. Iranian N being very far away.

A very short look at archaeology could have told you that as well.
Right



No, the 50/50 basis for Yamnaya hasn't changed.
Or was it Corded Ware with very small farmer input?
 
For all doubters of Steppe invasion into South Asia and India here is a genetic proof:
In South Asia, our dataset provides insight into the sources of Ancestral North Indians (ANI), a West Eurasian related population that no longer exists in unmixed form but contributes avariable amount of the ancestry of South Asians, (Supplementary Information, section 9) (Extended Data Fig. 4). We show that it is impossible to model the ANI as being derived from any single ancient population in our dataset. However, it can be modelled as a mix of ancestry related to both early farmers of western Iran and to people of the Bronze Age Eurasian steppe; all sampled South Asian groups are inferred to have significant amounts of both ancestral types. The demographic impact of steppe related populations on South Asia was substantial, as the Mala, a south Indian population with minimal ANI along the ‘IndianCline’ of such ancestry, is inferred to have ~18% steppe-related ancestry, while the Kalashof Pakistan are inferred to have ~50%, similar to present-day northern Europeans.
 
For all doubters of Steppe invasion into South Asia and India here is a genetic proof:

There was without a doubt Steppe influx into India the Out of India theory doesn't make much sense so I don't bother, however the figure of 50% for other South Asians is far too high even tribal Indians are shown wth ~18% Steppe admixture which is exactly the reason that brings the authors to the idea that something very EHG like did already exist in the region prior to the Indo_Iranian migration. So not all of the "Steppic" ancestry there is really Steppic but could be even more ancient.

And this would also explain where the ~13% EHG admixture in the mesolithic and calcolthic Iranian samples come from.
 
For all doubters of Steppe invasion into South Asia and India here is a genetic proof:

In South Asia, our dataset provides insight into the sources of Ancestral North Indians (ANI), a West Eurasian related population that no longer exists in unmixed form but contributes avariable amount of the ancestry of South Asians, (Supplementary Information, section 9) (Extended Data Fig. 4). We show that it is impossible to model the ANI as being derived from any single ancient population in our dataset. However, it can be modelled as a mix of ancestry related to both early farmers of western Iran and to people of the Bronze Age Eurasian steppe; all sampled South Asian groups are inferred to have significant amounts of both ancestral types. The demographic impact of steppe related populations on South Asia was substantial, as the Mala, a south Indian population with minimal ANI along the ‘IndianCline’ of such ancestry, is inferred to have ~18% steppe-related ancestry, while the Kalashof Pakistan are inferred to have ~50%, similar to present-day northern Europeans.

If Bronze-Age-Eurasian-steppe-like people were already in North India and early-farmers-of-Western-Iran migrated there we could have the same result.
 
This is what we've been waiting for.

I haven't had a chance to read this as an old college buddy passing through town compelled me to compromise my faculties for the past 18 hours.

A couple things.

I while ago I noticed that there was a surged in Teal in steppe EHG prior to any evidence of contact with the Caucuses. On this notion I proposed early contacts with the South East/Iranian Plateau. The evidence of a freakishly early neolithic on the Volga is also consistent with this.

Also I think Basal Eurasian comes from South Asia.
 
If Bronze-Age-Eurasian-steppe-like people were already in North India and early-farmers-of-Western-Iran migrated there we could have the same result.
Before bronze age Steppe people had different admixture signature, were genetically different from Bronze age steppe people. I'm sure the authors of this paper would recognize Steppe Bronze signature in Indian population from any other.
 
Any idea why Figure 1c is not in tune with Figure 4b? According to 1c Anatolian N is mixture of mostly Natufian/Levant farmer with WHG. According to 4b mostly Iranian N, then Levant N, and some WHG. 1b PCA chart also plots Anatolian and European farmer between position of Natufians and WHG. Iranian N being very far away.
There seems to be a serious discrepancy with prediction model and actual samples for Anatolian Neolithic. Look at Extended Data Figure 5, top of the page in the middle. The prediction model is much closer in agreement to what Figure 4 represents (Iranian N/Levant N/WHG), while actual data agrees more with Figure 1c (Levant/WHG). Is Figure 4 from some sort of prediction, and Figure 1c is actual data?
What am I missing here?
 
.

Also I think Basal Eurasian comes from South Asia.
Yep, as Alan said and I agree, it most likely comes from Arabian peninsula.
 
LeBrok, can you try the fst chart? It works for me.
 
I don't think there's any way of knowing at this stage where the Basal Eurasian was hiding, but one of the points against an Arabian refugia is that Levant Neolithic has less of it than Iranian hunter-gatherer (44% to 64%). On the other hand, both Levant Neolithic and Iranian Neolithic have about the same amount-44%-so the argument could be made that Basal was diluted in the west by something WHG like and in the east by something EHG or maybe ANE like.

The other alternative often mentioned is a Persian Gulf refugia, which is actually I think what Alan said?

@Holderlin,
I've considered that too. It would certainly explain why we haven't stumbled upon it yet, given that we have nothing really old from that region.

@Alan,
That makes sense to me, and I think the statements in the paper alluding to perhaps more "proximate" contacts was included. So, not that there wasn't actual steppe movement to India, but that there are older processes which may be inflating the figures.
 

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