The genetic structure of the world’s first farmers

[MOESAN]

I think as Y-R1 was surely born in Central Asia or not too far, some specific subclades reach Iran and Near-East-South Caucasus through the South Caspian Sea; some gave birth to the famous V88 and yet the precise place of this has to be proved what does not disprove its passage through Near East, others stayed South the Caucasus. But these above mentioned clades are not the ancestors of supposed "steppic" L23 or Z2103 or L51. Just a feeling, not proved at this stage.
It seems the bulk of these last three subclades lived their destiny without too numerous others Y-great haplos among them (R1a, J2 by instance) the R1b-M415 alias L278 of Kura-Araxes Bronze is too poorly defined or of a too "old nature" to tell us too much. Kura-Araxes seems a synthetic culture envolving Uruk people, Caucasians "autochtones" and perhaps some eastern influence of Eastern Caspian, so we are still in balance here.
Concerning EHG genes among CHG, my feeling is that it could be the result of ancient shared ancestral DNA rather than a typical admixture. All the way we see that as time passed the pops drifted and "specialized" or "localized" their auDNA and genuine Iran Neol would have had very little EHG DNA stayed in them, so the new recent EHG DNA has to be come from somewhere else, for I think. But I cannot exclude an other geographical origine than the Pontic Steppes even if it has my preference to date.

 

[Alan]

Holderin I have no dersire or time to discuss this any further. Just my adivce don't look just at the admixture charts, read the text and even some of the lazaridis tweets. In the text they say Iran_Meso is basically Iran_Neo + something EHG like.

 

[MOESAN]

Holderin I have no dersire or time to discuss this any further. Just my adivce don't look just at the admixture charts, read the text and even some of the lazaridis tweets. In the text they say Iran_Meso is basically Iran_Neo + something EHG like.

Yes, but Mesoi Iran is not Neol Iran! Either the last ones are not the exact descendants of the former, or they washed their genome after generations (it's a common phenomenon since Palleolithic: specialization and drift); it seems Iran Chalcol was poor in EHG too.. THese Armenian Chalco guys had also some EEFlike or Levant-Anatolianslike DNA, which added to their rather southeastern haplos Y-L1a, show a very puzzling sketche of the elites of the time! AT first sight it doesn't point to a pure Iran pop introgression. But at the difference than others I don't conclude too quickly here what make a boring forumer of mylself: eastern males could have mixed with females come from other horizons in a period of heavy changes and material progresses which could have acted as crossings promotors.
I know, we are looking for simple enough shcemes and realtiy is showing us very more complicated things concerning some individuals who are not by force the most representative of the whole of the pops in cause at those times. And the clannic system of the male elites of those times make my own bets very unsure: my intuitive "pure" Y-R1b-preL23 come only through North Caspian could be parlty an error because some clans (L23>>L51) could have reached the Pontic region through Caucasus as well preserved males clans (# Z2103 ones), spite the melting-pot region they would have crossed!
So, let's wait for even more DNA (famous song).

 

[Alan]

Yes, I know. It's an old subclade. Although we still have the fact that the oldest R1b samples are being found on the steppe and in Europe and we also have an R* in ancient Siberia. So the current data is still hinting at the steppe or europe, bronze age expansions aside.

Once again no we do not have the oldest subclades in the Steppes. Please stop giving misinformations.

The oldest up to date sampled R1a and R1bs are in the Steppes but they are not the oldest subclades means they are all upstream to basal R1a l62 and R1b m343. Which have been found among Kurds and on the Iranian Plateau. Those therefore can not be explained via Steppes, because EVEN if they were found in Eneolithic Samara they were not part of the Indo European expansion from the Steppes.

 

[Tomenable]

Coming back to Basal Eurasians, and their original Y-DNA haplogroups:

What do you think about this model (with haplogroup CT splitting into DE and CF before leaving Africa, and then D and E migrating from Africa to Arabia - becoming "Basal Eurasians" later on - while C and F migrating to the Levant, admixing with Neanderthals):

Direct link to map

 

[holderlin]

the oldest R1b samples are being found on the steppe and in Europe and we also have an R* in ancient Siberia. So the current data is still hinting at the steppe or europe, bronze age expansions aside.

Once again no we do not have the oldest subclades in the Steppes. Please stop giving misinformations.

This is what I'm talking about. You're not reading what I wrote. You're just making stuff up. The oldest R1b samples have in fact been found on the steppe and in Europe.

I'm aware of the modern distributions of R1b and R1a subclades.

 

[Tomenable]

The oldest sample of R1b known so far is from North Italy (Villabruna): 14,180 - 13,780 years old.

The oldest sample of R1a known so far is from Karelia (Red Deer Island): 8,800 - 7,950 years old.

 

[bicicleur 2]

Coming back to Basal Eurasians, and their original Y-DNA haplogroups:

What do you think about this model (with haplogroup CT splitting into DE and CF before leaving Africa, and then D and E migrating from Africa to Arabia - becoming "Basal Eurasians" later on - while C and F migrating to the Levant, admixing with Neanderthals):

Direct link to map

the Nubyan Complex existed in southern Arabia > 106 ka
these were the ancestors of the modern Eurasians
that was before the BT TMRCA
so this was haplo BT
and haplo B and E are both backmigrations to Africa
the Neanderthal admixture happened 60-55 ka
that was after the DE and CF splits, so not necesarily all 4 clades got Neanderthal admixture
actually 4.5 Mota E in Ethiopia didn't have Neanderthal admix

the humans that lived in the Levant 110-90 ka did admix with Neanderthals, but went extinct
it is their admixed DNA that was found in the Altaï Neanderthals

 

[Tomenable]

the humans that lived in the Levant 110-90 ka did admix with Neanderthals, but went extinct
it is their admixed DNA that was found in the Altaï Neanderthals

Are you sure that the Nubyan Complex did not end up like this as well ???

the Nubyan Complex existed in southern Arabia > 106 ka
these were the ancestors of the modern Eurasians

See above.

IMO they weren't ancestors of modern Eurasians, but a "failed" population, which got extinct. They were the ones who got slaughtered by Neanderthals or / and by the Toba Eruption 74,000 years ago, alongside with those from the Levant.

Some of them made it to Australia, and remnants of their mtDNA were found near Kow Swamp and Lake Mungo.

It was mtDNA which was not descended from "mitochondrial Eve", but diverged shortly before Eve.

 

[holderlin]

The oldest sample of R1b known so far is from North Italy (Villabruna): 14,180 - 13,780 years old.

The oldest sample of R1a known so far is from Karelia (Red Deer Island): 8,800 - 7,950 years old.

Yes, thank you.

Not to mention all of the Bronze age R1b/a in Europe and the R1b/a on the steppe spanning from mesolithic to bronze age.

 

[Angela]

Razib Khan has a piece up on the paper. It starts off with some very fulsome praise for Iosif Lazaridis.
http://www.unz.com/gnxp/the-great-human-disruptions/#comment-1480355

"He should frame it; it's quite some accolade.

"One can appreciate a work of art on two levels....on some level we acknowledge physical beauty when we see it, before we even think it.*

Another level of appreciation is narrower, and that is one where you have awareness of the ingenuity of technique, the deep virtuosity and fluency of execution. This aspect of understanding aesthetics is naturally delimited to those with equivalent skills, or whose skills aspire toward the plane of the masters...Reading Iosif Lazaridis’ The genetic structure of the world’s first farmers you can evaluate on both levels. The results are broadly accessible, but the depth of the analysis is clear to anyone who has ever attempted something analogous. These papers coming out of David Reich’s lab have a certain template, but they are definitely not paint-by-numbers. For those who are interested in technical details, you have to read the supplements."

I don't aspire to that plane, but I think I know enough to appreciate it.

As to the substance:
"Ancient DNA has revealed that genetic variation in the human past has been characterized by very strong discontinuities, both over time and space."

"It turns out that a majority of the ancestry of modern Europeans is likely exogenous to the continent over the last ~10,000 years. "

"The evidence which is coming back clearly is that pre-modern populations exhibited a great deal of genetic differentiation over even small distances, and, that differentiation could persist for thousands of years."

"Basically, all West Eurasian populations today can be modeled to a first approximation as a mixture of four ancestral groups which flourished on the order of ~10,000 years ago."

I think most people would agree with that. Some of his other claims I could quibble with, such as:

"Between group proportions of variation on the order of 10% of the total variance, what you see between Europeans and Han Chinese, were not atypical for nearby peoples in the past."

As someone pointed out in the comments, the fst between Europeans and Chinese is smaller than that.

"These two groups seem to have stumbled upon agriculture very near to each other at similar times.Where they independent events? I suspect that they weren’t. I’m not implying here cultural diffusion. There is evidence of independent domestication of landraces in the Zagros. Rather, these two populations were part of a broader network of trade connections within a similar ecological landscape. It was not coincidental that both stumbled upon agriculture. Likely there was diffusion between the two of similar cultural precursors to agriculture. Their location in such proximity and emergence onto the world scene can not be coincidence, though the details are to be worked out."

There had to have been cultural diffusion, and after the very early Neolithic some demic diffusion too, or how did the farmers who left for Europe get the full complement of domesticated animals that are the hallmark of the "other" Neolithic. How did Anatolian Neolithic get its Levantine Neolithic, and vice versa. How, also, can the EN be modeled with either some CHG or some Iran Neolithic, at least the Neolithic that wound up in Europe, if not Cardial?

I also don't think they "stumbled" onto it. They were in the right place at the right time, and human ingenuity and perseverance did the rest.

Khan also reiterates once more that all these migrations must have included inter-group conflict. Perhaps, but maybe not always or not to the same extent in each one.

I'm also not sure if he means to say all of yDna Haplo "E" originated in West Eurasia, or just a big chunk of the downstream clades. the ones present in Egypt, the Horn, North Africa, etc. Certainly, it has implications for discussions of Afro-Asiatic.

 

[bicicleur 2]

he names 4 cornerstone populations as the paper does, but he replaces the Levantine neolithic by EEF, which acording to the paper is a mixture of Levant N, Iran N and some WHG
the identity of the Anatolian/European farmer remains a mystery to me, it doesn't match Levant N nor Iran N
also, what strikes me : over 60 % of Anatolian/European farmer were G2a2 while none of them have been found in the whole study

I find this interesting : The genetic differentiation began once the expansion phase ceased, and groups began to struggle for existence at the Malthusian limit.

once farmers settle, they stop moving and they become isolated
is this why European farmers were so quickly and easily replaced by the mobile corded ware people?

my opinion on haplo E and Afro-Asiatic is here http://www.eupedia.com/forum/threads/32412-Natufian-E1b1b1-spoke-proto-Afroasiatic

 

[Alan]

Razib Khan has a piece up on the paper. It starts off with some very fulsome praise for Iosif Lazaridis.
http://www.unz.com/gnxp/the-great-human-disruptions/#comment-1480355

"He should frame it; it's quite some accolade.

"One can appreciate a work of art on two levels....on some level we acknowledge physical beauty when we see it, before we even think it.*

Another level of appreciation is narrower, and that is one where you have awareness of the ingenuity of technique, the deep virtuosity and fluency of execution. This aspect of understanding aesthetics is naturally delimited to those with equivalent skills, or whose skills aspire toward the plane of the masters...Reading Iosif Lazaridis’ The genetic structure of the world’s first farmers you can evaluate on both levels. The results are broadly accessible, but the depth of the analysis is clear to anyone who has ever attempted something analogous. These papers coming out of David Reich’s lab have a certain template, but they are definitely not paint-by-numbers. For those who are interested in technical details, you have to read the supplements."

I don't aspire to that plane, but I think I know enough to appreciate it.

As to the substance:
"Ancient DNA has revealed that genetic variation in the human past has been characterized by very strong discontinuities, both over time and space."

"It turns out that a majority of the ancestry of modern Europeans is likely exogenous to the continent over the last ~10,000 years. "

"The evidence which is coming back clearly is that pre-modern populations exhibited a great deal of genetic differentiation over even small distances, and, that differentiation could persist for thousands of years."

"Basically, all West Eurasian populations today can be modeled to a first approximation as a mixture of four ancestral groups which flourished on the order of ~10,000 years ago."

I think most people would agree with that. Some of his other claims I could quibble with, such as:

"Between group proportions of variation on the order of 10% of the total variance, what you see between Europeans and Han Chinese, were not atypical for nearby peoples in the past."

As someone pointed out in the comments, the fst between Europeans and Chinese is smaller than that.

"These two groups seem to have stumbled upon agriculture very near to each other at similar times.Where they independent events? I suspect that they weren’t. I’m not implying here cultural diffusion. There is evidence of independent domestication of landraces in the Zagros. Rather, these two populations were part of a broader network of trade connections within a similar ecological landscape. It was not coincidental that both stumbled upon agriculture. Likely there was diffusion between the two of similar cultural precursors to agriculture. Their location in such proximity and emergence onto the world scene can not be coincidence, though the details are to be worked out."

There had to have been cultural diffusion, and after the very early Neolithic some demic diffusion too, or how did the farmers who left for Europe get the full complement of domesticated animals that are the hallmark of the "other" Neolithic. How did Anatolian Neolithic get its Levantine Neolithic, and vice versa. How, also, can the EN be modeled with either some CHG or some Iran Neolithic, at least the Neolithic that wound up in Europe, if not Cardial?

I also don't think they "stumbled" onto it. They were in the right place at the right time, and human ingenuity and perseverance did the rest.

Khan also reiterates once more that all these migrations must have included inter-group conflict. Perhaps, but maybe not always or not to the same extent in each one.

I'm also not sure if he means to say all of yDna Haplo "E" originated in West Eurasia, or just a big chunk of the downstream clades. the ones present in Egypt, the Horn, North Africa, etc. Certainly, it has implications for discussions of Afro-Asiatic.

Network of trade is a key point and I say this implies also to the Indo EUropeans. What we call the PIE were probably a network of cultures in close contact.

 

[Alan]

he names 4 cornerstone populations as the paper does, but he replaces the Levantine neolithic by EEF, which acording to the paper is a mixture of Levant N, Iran N and some WHGant N nor Iran N
also, what strikes me : over 60 % of Anatolian/European farmer were G2a2 while none
the identity of the Anatolian/European farmer remains a mystery to me, it doesn't match Lev of them have been found in the whole study

I find this interesting : The genetic differentiation began once the expansion phase ceased, and groups began to struggle for existence at the Malthusian limit.

once farmers settle, they stop moving and they become isolated
is this why European farmers were so quickly and easily replaced by the mobile corded ware people?

my opinion on haplo E and Afro-Asiatic is here http://www.eupedia.com/forum/threads/32412-Natufian-E1b1b1-spoke-proto-Afroasiatic

Indeed you can't model, West Eurasia just based on these four cornerstones. Levant_N themselves seem to be basically Natufian + some WHG like and Iran_Neo like admixture.

You need to see Anatolian_Neo as it's own cornerstone, because it is decisive to determine the farmer ancestry in Europeans. otherwise you will get flawed results.

We are dealng here with at least three, if not four with CHG, cornerstones in ancient West Asia. Anatolian_Neo, Iran_Neo(+CHG) and Levant_Neo.

 

[bicicleur 2]

Indeed you can't model, West Eurasia just based on these four cornerstones. Levant_N themselves seem to be basically Natufian + some WHG like and Iran_Neo like admixture.

You need to see Anatolian_Neo as it's own cornerstone, because it is decisive to determine the farmer ancestry in Europeans. otherwise you will get flawed results.

We are dealng here with at least three cornerstones in ancient West Asia. Anatolian_Neo, Iran_Neo(+CHG) and Levant_Neo.

exactly, that is my perception too

 

[Hauteville]

When the genetists move to search into South Europe in the next years we can see how much J2 and R1b there were in the very old times. My two cents.

 

[kingjohn]

nice map :

 

[IronSide]

Who are the Basal Eurasians ? where did they come from ? what was their original Y-dna ?

Haplogroup E was the obvious suspect given its "basal" position in the Y-tree, but Iran Neolithic didn't have it, and they had more basal than the Natufians.

Haplogroup G can also be considered "basal" on Y-tree, but faces the same problem as E, it hasn't been found in Natufians, but in Iran Neolithic.

So who were they ? if not men .. then maybe women ? mt-Haplogroup N1 is common to many Neolithic cultures in the Middle East and Europe, haplogroup X and R0a can also be considerd "basal" and they were common in east and west.

A crazy thought, those amazon founders of civilization .. the original goddesses, I remembered the 12,000-years-old grave of a significant Natufian female, no wonder all Neolithic deities (if the figurines were intended to be divine) were female.

Is it also a coincidence that both founder Neolithic cultures (Iran and Levant) developed agriculture in such proximity and yet be so different ?

 

[bicicleur 2]

Who are the Basal Eurasians ? where did they come from ? what was their original Y-dna ?
Haplogroup E was the obvious suspect given its "basal" position in the Y-tree, but Iran Neolithic didn't have it, and they had more basal than the Natufians.
Haplogroup G can also be considered "basal" on Y-tree, but faces the same problem as E, it hasn't been found in Natufians, but in Iran Neolithic.
So who were they ? if not men .. then maybe women ? mt-Haplogroup N1 is common to many Neolithic cultures in the Middle East and Europe, haplogroup X and R0a can also be considerd "basal" and they were common in east and west.
A crazy thought, those amazon founders of civilization .. the original goddesses, I remembered the 12,000-years-old grave of a significant Natufian female, no wonder all Neolithic deities (if the figurines were intended to be divine) were female.
Is it also a coincidence that both founder Neolithic cultures (Iran and Levant) developed agriculture in such proximity and yet be so different ?

Basal Eurasians, my guess?
A group whose Y and mt DNA went extinct.
Todays Y and mtDNA is from a group of people that expanded from SW Asia into Eurasia 50 ka.
But 125 ka, there were already humans in Jebel Faya. They expanded too. 73 ka in Jwalapuram, India, 80 ka in southern China and 65 ka in Kakadu National Park, Australia.
After the 50 ka expansion from SW Asia, their Y and mtDNA went extinct.
But some of their autosomal survived. Their autosomal was Basal Eurasian.
And haplo G and H2 brought this autosomal back from India to SW Asia during LGM, when the Thar desert expanded.

Iran and the Levant had 2 very different agricultures.
The Levant farmers grew cereals.
The Iran herders had goat, sheep, pigs and cattle, and supplemented that with some pulses.
With PPNB, both blended in the Levant. Y-DNA T and mtDNA X had arrived in the Levant.

 

[IronSide]

Basal Eurasians, my guess?
A group whose Y and mt DNA went extinct.
Todays Y and mtDNA is from a group of people that expanded from SW Asia into Eurasia 50 ka.
But 125 ka, there were already humans in Jebel Faya. They expanded too. 73 ka in Jwalapuram, India, 80 ka in southern China and 65 ka in Kakadu National Park, Australia.
After the 50 ka expansion from SW Asia, their Y and mtDNA went extinct.
But some of their autosomal survived. Their autosomal was Basal Eurasian.
And haplo G and H2 brought this autosomal back from India to SW Asia during LGM, when the Thar desert expanded.

Iran and the Levant had 2 very different agricultures.
The Levant farmers grew cereals.
The Iran herders had goat, sheep, pigs and cattle, and supplemented that with some pulses.
With PPNB, both blended in the Levant. Y-DNA T and mtDNA X had arrived in the Levant.

Interesting theory, may be true, but you've got to admit mine is more romantic heroic wise amazons hahahaha