The genetic structure of the world’s first farmers

[Tomenable]

Haplogroup R2 in Iran (Ganj Dareh) could be related to ANE ancestry.

 

[Alan]

Genetiker wrote that Afontova Gora 2 who lived in Siberia 17,000 years ago was derived for SLC24A5 white skin mutation:

"(...) Mal’ta 1 had two copies of the ancestral allele of rs1426654, but Afontova Gora 2, an Upper Paleolithic hunter-gatherer who lived 17,000 years ago in Siberia, had two copies of the derived allele. This SNP is located in the gene SLC24A5, and its derived allele is one of the two major Caucasoid depigmentation mutations. The other major Caucasoid depigmentation mutation is the derived allele of rs16891982, in the gene SLC45A2. (...)"

So it seems that Caucasoid skin-lightening alleles originated from ANE. Was ANE admixture present in Neolithic Near East?

Because EHG definitely had ANE admixture. And SHG also had it (they were part-EHG). IIRC, CHG also had some ANE.

According to this Lazaridis paper Mal'ta sample itself is ~28% Iran_meso/neo and 10% CHG like (or derived from it) according to the graph with the pca plot in the study, you can look it up.

 

[Tomenable]

But Mal'ta (24,000 years old) was brown-skinned. Afontova Gora 2 lived ~7,000 years after Mal'ta.

Native Americans don't have Caucasoid light skin mutations despite having Mal'ta related ancestry.

So if this mutation originated among ANE, it was probably between 24,000 and 17,000 years ago.

 

[Angela]

Yes and when they moved North and especially later when the adopted a Vitamin D poor Neolithic_Diet, the became fairer. The combination of Genes+enviroment+diet is the key.

Exactly. That's what the science we have so far would suggest.

Also, of course, there's the fact that the Key paper didn't at all discuss SLC24A5, the oldest example of which can be found in the CHG hunter-gatherer from around the Caucasus if I remember correctly, at least in terms of an academic analysis.

 

[Angela]

Has anyone given any thought to the description of EHG as something like a combination of WHG plus something on the Onge-Han scale? We know from other analyses that EHG has an "eastern" affinity. What exactly does that say about ANE?

Sorry, I haven't got the exact quote to hand.

As to the origin of PIE, I think the main development and spread was from the Pontic-Caspian steppe. I'm just not sure about proto-PIE. If Anatolian developed south of the Caucasus, or even in the Caucasus itself, then technically PIE did not originate on the Pontic-Caspian lsteppe. I'm not sure about that, however.

All the studies about the location where PIE would first have developed, i.e. in terms of the words for flora and fauna, could that kind of locale also be found east of the Caspian or even near modern day Armenia or the Iranian plateau?

Also, when talking about influences by other languages, is the influence of the Uralic languages the same in Anatolian as it is in other IE languages? Also, where exactly were the Uralic languages located at this time. How far south did they extend?

 

[Tomenable]

Selective sweep could happen after the adoption of farming. But this tells us nothing about the place of origin of these mutations. For example it is possible that 5% (1/20) of Upper Paleolithic Europeans were light-skinned. But only later a selective sweep took place and 99% became light-skinned (as is the case today). Some scholars suggest that it was actually sexual selection.

Why has no such selective sweep took place in the Middle East, by the way?

Or it took place in the past, but modern Near Easterners are darker due to mixing with Arabs and SSA ???

 

[Tomenable]

EHG as something like a combination of WHG

I really doubt that EHG had actual WHG admixture. It was probably just some "WHG-like" ancestry, but not actual WHG.

It is probably a similar case as with Corded Ware having Yamna ancestry, while in reality it could be just "Yamna-like".

 

[Angela]

Exactly. That's what the science we have so far would suggest.

Also, of course, there's the fact that the Key paper didn't at all discuss SLC24A5, the oldest example of which can be found in the CHG hunter-gatherer from around the Caucasus if I remember correctly, at least in terms of an academic analysis.

I don't know how many times it has to be said. Light skin, in the sense of "European" light skin, did not exist in UP Europeans or the WHG. Pop those values into a predictor and you will not get a prediction for light skin. Partly it's because the WHG had precursor alleles but not the target alleles themselves. The other factor is that it takes the combination of these snps to produce it, not just one or two.

As I've said ad nauseam, the major depigmentation snps may have occurred in two different populations. It's the convergence which is crucial, that and then the environmental factors, physical and social, which acted upon the mutations.

Part of any sweep is going to entail a convergence of not only the gene mutation but the climate, and in some cases perhaps diet, not to mention any social selection that may go on. If you're living in Anatolia you might get as much Vitamin D from the sun as you need from derived copies of SLC24A5 even if you have no or one copy of derived SLC 45A2. Of course, migration from other, "darker" areas is also going to be a factor.

 

[davef]

@Angela

You wrote:
"I don't know how many times it has to be said. Light skin, in the sense of "European" light skin, did not exist in UP Europeans or the WHG. Pop those values into a predictor and you will not get a prediction for light skin. Partly it's because the WHG had precursor alleles but not the target alleles themselves. The other factor is that it takes the combination of these snps to produce it, not just one or two."

Cliff notes version: the hunter gatherers had one set of alleles for white skin and came into contact with a population with the other set of alleles (farmers) and produced offspring with both of the allele sets required to have "white skin". Right?

 

[Sile]

As we are taught in Australia

Farming created light skin because grains gives a person zero vitamin D

Grains in the diet decrease calcium absorption, thus increasing the demand for vitamin D

so hunters stayed dark skin as meat gave them vitamin D, farmers became light skins because they got no Vitamin D from farming

dark skinned farmers came from the north of the zargos mountains, saw the fertile crescent and decided to farm, over time they became light skinned

 

[MOESAN]

Do we know exactly what farmers ate? Surely corns but not only. It seems they hunted too and so had meat. Surely less than Hgs but those ones ate berries and not-meat food too? And farmers drunk milk, I think. Perhaps could one of us precise this? So selection, but surely not so simply based.

 

[Tomenable]

did not exist in UP Europeans or the WHG.

But it did exist in ANE (Afontova Gora 2) andl later in Mesolithic EHG & SHG. So it looks like being Siberian in origin. Of course I mean the "Caucasoid" variant, not the "Mongoloid" one - which probably originated even farther to the north-east (although Upper Paleolithic Kostenki14 from European Russia had the "Mongoloid" variant of light skin mutation, according to Genetiker).

 

[Tomenable]

it takes the combination of these snps to produce it, not just one or two.

There is a gradation of skin tones in Europeans (but most of Europeans have shades from columns 1, 2, 3, 4). The combination of all SNPs will produce shade A1, which is the lightest; with lack of some SNPs, it will be e.g. E1 (still very light):

 

[Tomenable]

^^^ Just 2 genes (!) are not enough to explain such a huge variety of skin tones.

I am sure that many more genes are influencing skin pigmentation in humans.

 

[MOESAN]

Do we know exactly what farmers ate? Surely corns but not only. It seems they hunted too and so had meat. Surely less than Hgs but those ones ate berries and not-meat food too? And farmers drunk milk, I think. Perhaps could one of us precise this? So selection, but surely not so simply based.

 

[Angela]

Do we know exactly what farmers ate? Surely corns but not only. It seems they hunted too and so had meat. Surely less than Hgs but those ones ate berries and not-meat food too? And farmers drunk milk, I think. Perhaps could one of us precise this? So selection, but surely not so simply based.

Vitamin D occurs naturally in very few foods. Milk has very little Vitamin D. It has it today because it is fortified with it. Likewise, meat in general doesn't have very much, but organ meats have more. The biggest source of it is in fish, particularly oily fish.

See:
https://ods.od.nih.gov/factsheets/VitaminD-HealthProfessional/


In some hunter-gatherer groups in Europe they got 80% of their caloric intake from meat and fish. Around the Baltic a very large percentage of that 80% was from fish. In some Neolithic societies the percentages were almost exactly reversed, although it varied by area. I've previously posted papers on all of this. Consumption of cow meat (domesticated) seems to have been more for celebrations and other ritual purposes. The liver is a very small part of the cow, of course. Pork has more and they did consume some pigs, but again, it would have been fish consumption which would have made a big difference.

In the book "The Early Mediterranean Village", Robb makes much of the fact that although there were fresh water lakes near some of these Italian Neolithic settlements there is no evidence that the Neolithic farmers actually ate fish. It almost seemed to him like a deliberate aversion. In other areas there was some hunting and some fishing, but by no means in all. Later on, with downturns in the climate, or, who knows, with some admixture with some remnants of the WHG, there was some increased reliance on hunting and fishing.
http://www.cambridge.org/cu/academi...e-and-social-change-neolithic-italy?format=PB

There is also a paper which I previously posted showing that even in Scandinavia and the Baltic people who had previously based most of their diet on fish stopped eating it when they turned to agriculture. It was only later, perhaps with the collapse of the Neolithic package, that they turned to the sea again for food. I've wondered, as Frachetti seemed to indicate in his books and articles whether grain took on an almost ritual significance.

 

[arvistro]

Has anyone given any thought to the description of EHG as something like a combination of WHG plus something on the Onge-Han scale? We know from other analyses that EHG has an "eastern" affinity. What exactly does that say about ANE?

Sorry, I haven't got the exact quote to hand.

As to the origin of PIE, I think the main development and spread was from the Pontic-Caspian steppe. I'm just not sure about proto-PIE. If Anatolian developed south of the Caucasus, or even in the Caucasus itself, then technically PIE did not originate on the Pontic-Caspian lsteppe. I'm not sure about that, however.

All the studies about the location where PIE would first have developed, i.e. in terms of the words for flora and fauna, could that kind of locale also be found east of the Caspian or even near modern day Armenia or the Iranian plateau?

Also, when talking about influences by other languages, is the influence of the Uralic languages the same in Anatolian as it is in other IE languages? Also, where exactly were the Uralic languages located at this time. How far south did they extend?

Where Anatolian disagrees with late PIE reconstruction it agrees with Indo-Uralic one, I.e. Tu (you, late PIE) vs Ti (Anatolian, Proto-Uralic and Indo-Uralic). Klokhorst or similar surname had article on this.
As to Uralic themselves, they were not there as Uralic back then. There were different Indo-Uralic dialects, one of which got mixed with North Caucasian and other way later developed into Proto-Uralic.
Is not clear how far South they were then, but judged by PIE, they knew domesticated animals, did not know agriculture, knew (some) metals (Gold, Silver and metal), did not know metallurgy.

 

[Angela]

Where Anatolian disagrees with late PIE reconstruction it agrees with Indo-Uralic one, I.e. Tu (you, late PIE) vs Ti (Anatolian, Proto-Uralic and Indo-Uralic). Klokhorst or similar surname had article on this.
As to Uralic themselves, they were not there as Uralic back then. There were different Indo-Uralic dialects, one of which got mixed with North Caucasian and other way later developed into Proto-Uralic.
Is not clear how far South they were then, but judged by PIE, they knew domesticated animals, did not know agriculture, knew (some) metals (Gold, Silver and metal), did not know metallurgy.

So, do we know if a population inhabiting, say, the Caucasus or just south of it, or living near the Caspian could have come into contact with Proto-Uralic speakers or a "language" that later developed into proto-Uralic?

 

[MOESAN]

Alan;482392]The EHG admixture in Copper Age Iran equals that found in mesolithic CHG.


Well, not if we go by this chart, but the level of EHG in Armenia Copper Age is pretty close to that in CHG.*






Well, it decreases in the Early Bronze Age, but it increases to the highest levels in the Middle/Late Bronze Age, so by then, whatever was the case in previous eras, there might have been movement from north of the Caucasus.


I agree that it's complicated, and I don't see this as a simple matter of steppe intrusion. Part of the difficulty in interpreting what we see is that we don't have an Armenian Neolithic sample. The other problem, as Lazaridis pointed out in his post, is that we don't know the geographical range of these ancient people.


Let's assume, for the moment, that CHG resulted from the admixture of a population similar to the Iranian Neolithic who moved slightly north and encountered EHG. Did they encounter EHG already south of the Caucasus? Or were the EHC only north of the Caucasus, but the resulting admixed population straddled the entire Caucasus range. These are things we don't yet know and may perhaps never know.


By the Armenian Chalcolithic we actually see, as you say and as I pointed out upthread, that EHG has decreased at the expense of an intrusion of Levant Neolithic and WHG. Is that actually just a breakdown of the Anatolian Neolithic that arrived from the west? Does that make more sense than a migration of purely Levant Neolithic people all the way north?


Then in the Armenia Early Bronze the EHG declines yet again, perhaps by admixture by a population heavier in Iranian Neolithic?


Only in the Armenia Late Bronze Age do we see the EHG levels rise back to the levels of the Iran Chalcolithic. That's the strongest case for steppe intrusion, in my opinion.

We need Armenian N!
OK for a possible Anatolian contribution concerning WHG+LevtN (every new simulation sends new reference population, funny indeed!) intoArmenia: why not?
Concerning comparions metals age Armenia with CHG, as Armenia shows levels of WHG and LevtN, if Armenia was issued from old CHG, this new admixture would reduce the EHG and IranN (=CHG) in itself. Or if Armenia was previously a mix of WHG and LevtN (=Anatolia)+ the admixture with CHGs from N-Caucasus would also produce less EHG in itself tha in the donor CHG pop. So I think and CHG and Armenia had high levels of IranN, but Armenia received new EHG non-Caucasus, so surely Steppic. Some papers all the way seem showing metals ages Armenia had affinities with Yamnaya, not only 'westasian'; Genetiker whatever the worth of his work, "found" some East-Asia (rather 'amerind' or 'siberian') in BA Armenians what does not seem come through iran at these dates but was found in almost every supposed Steppic influenced pops. On a plotting of Davidsky BA Armenians are shifted towards Lezgins, and Tadjiks, closer to these last ones than Georgians or Adygei, far from the today Armenians and even Iranians. I 'm not sure all that would be without any signification at all? and EHG of some weight in CSW Asia at these dates? I don't buy before more infos.
We could say, it's true, that the supposed "steppic" admixture would not prove a cultural influence of North Caucasus upon South, but rather an osmosis after colonization of North by South Caucasus? Who knows? All the way I discard a colonization by Tadjiks from East at those times, for good sense and archeological reasons.

 

[Garrick]

Sorry, I haven't got the exact quote to hand.

As to the origin of PIE, I think the main development and spread was from the Pontic-Caspian steppe. I'm just not sure about proto-PIE. If Anatolian developed south of the Caucasus, or even in the Caucasus itself, then technically PIE did not originate on the Pontic-Caspian lsteppe. I'm not sure about that, however.

All the studies about the location where PIE would first have developed, i.e. in terms of the words for flora and fauna, could that kind of locale also be found east of the Caspian or even near modern day Armenia or the Iranian plateau?

Also, when talking about influences by other languages, is the influence of the Uralic languages the same in Anatolian as it is in other IE languages? Also, where exactly were the Uralic languages located at this time. How far south did they extend?

From current perspective Anatolian, Steppe and Armenian hypotheses are in the game. Even synthesis of these hypotheses is possible.

After acquiring new knowledge including study Hak et al (2015), Balkan hypothesis is probably outdated. We can exclude Indigenous Aryan hypothesis too.

Paleolithic Continuity hypothesis has value, but for language generally, positing the presence Indo-European and non Indo-European languages in Europe from Paleolithic times.

Impact of Uralic languages existed. Also, impact of languages from the Caucasus existed. Indo European borrowed words from both families.

So IE and Uralic can have close relations. But Alan is right, Eurasiatic hypothesis which relates more Eurasian families: IE, Uralic, and other familes in northern and western Eurasia is controversial. We have another hypothesis - Nostratic, which relates IE, Kartvelian, Uralic, Altaic, and many other, even Afroasiatic families, and of course it is controversial too.
...

In this seminal paper by Lazaridis et al. another question is interesting too. It is about Natufian language. From this perspective Natufian language probably was some kind proto Afro-Asiatic. But I would like see other opinions.