The genetic structure of the world’s first farmers

[epoch]

Very nice new paper up. Dynamite: Natufians were only half Basal Eurasian and Basal Eurasian appears to have had no Neanderthal! Furthermore, the CHG part of Steppe appears to be made of Caucasian HG and part Iranian Chalcolithic. Fitted mixture proportions are 52.7% EHG, 18.1% CHG, 29.2% Iran_Ch.

Preprint: http://biorxiv.org/content/early/2016/06/16/059311
Supp Info: http://biorxiv.org/content/early/201...1.figures-only

The Neanderthal is very interesting as well. O, and Basal is not African. It is buried somewhere in the supp info tables.

EDIT: Y-DNA of Natufians were E1b and some J1. Iran G1a G2a and some J.

[Fire Haired14]

Y DNA results. All but a few Neolithic Levant samples had E1b, no suprise. Most had M123 though not M78(like most E1b in Europe and West Asia today).

Armenia_ChL (Chalcolithic Armenia)

I1407: L1a
I1632: L1a
I1634: L1a


Iran_Mesolithic (Hotu Cave)


I1293: J(xJ2a1b3, J2b2a1a1)


Iran_N


I1945: P1(xQ, R1b1a2, R1a1a1b1a1b, R1a1a1b1a3a, R1a1a1b2a2a)


My guess here is that this is R2, and hopefully we shall see when the bam files are released.


I1949: CT


Iran_LN


I1671: G2a1(xG2a1a)


Iran_ChL (Chalcolithic Iran)


I1662: J(xJ1a, J2a1, J2b)
I1674: G1a(xG1a1)


Natufians


I0861: E1b1b1b2(x E1b1b1b2a, E1b1b1b2b)
I1069: E1b1(xE1b1a1, E1b1b1b1)
I1072: E1b1b1b2(xE1b1b1b2a, E1b1b1b2b)
I1685: CT
I1690: CT


Levant_N


I0867: H2 (PPNB)
I1414: E(xE2, E1a, E1b1a1a1c2c3b1, E1b1b1b1a1, E1b1b1b2b) (PPNB)
I1415: E1b1b1 (PPNB)
I1416: CT (PPNB)
I1707: T(xT1a1, T1a2a) (PPNB)
I1710: E1b1b1(x E1b1b1b1a1, E1b1b1a1b1, E1b1b1a1b2, E1b1b1b2a1c) (PPNB)
I1727: CT(xE, G, J, LT, R, Q1a, Q1b) (PPNB)
I1700: CT (PPNC)


Levant_BA


I1705: J1(xJ1a)
I1730: J(xJ1, J2a, J2b2a)

[epoch]

The reduced Neanderthal in Basal... It has me thinking. Could that be the cause for the perceived increasing middle-eastern in WHG? It would be a nice way to explain for the slight increase in El Miron. Also, it shows that either Basal wasn't surviving in the Asian part of the Middle-East and thus the Basal Urheimat (I am laughing as I type these words ;.) must have been Egypt, or the Neanderthal admixture took place more north.

[bicicleur]

big surprises in unchartered territory
very interesting but I'll need some time to digest

[Fire Haired14]

The reduced Neanderthal in Basal... It has me thinking. Could that be the cause for the perceived increasing middle-eastern in WHG? It would be a nice way to explain for the slight increase in El Miron. Also, it shows that either Basal wasn't surviving in the Asian part of the Middle-East and thus the Basal Urheimat (I am laughing as I type these words ;.) must have been Egypt, or the Neanderthal admixture took place more north.

Reduced Neanderthal in Basal makes a lot of sense. WHG and El Miron didn't have Basal Eurasian ancestry. East Asians are equally close to them as to earlier Europeans, confirming they don't have Basal Eurasians.

[bicicleur]

Natufians are E-Z830 x(E-M123, M293), TMRCA 19.2 ka
That leaves open 2 possibilities : E-Z830* or E-V42.
That is : Natufians are extinct or surviving in Ethiopia ????

[bicicleur]

no G2a2 found, none
is G2a2 exclusive to Anatolian & European neolithic?

[bicicleur]

Reduced Neanderthal in Basal makes a lot of sense. WHG and El Miron didn't have Basal Eurasian ancestry. East Asians are equally close to them as to earlier Europeans, confirming they don't have Basal Eurasians.

Mota Cave HG E1b1a didn't have Neanderthal, probably Natufian E-Z830 didn't have either before coming to Asia.
It hints at arrival of E-Z830 from Africa.

I'm not sure Basal Eurasian originated in Africa though.
The reduced Neandertahl may be related to admixture with E-Z830 and unrelated to the Basal Eurasian.

[Fire Haired14]

@Angela,

Genetic continuum in Iran from Mesolithic to Neolithic.

The origin of the Neolithic of Iran does not appear to be related to either Anatolia or the Levant, as theNeolithic and Mesolithic of Iran are symmetrically related to either population (Fig. S7.5), providingno evidence for gene flow from either region into the Zagros, but hinting strongly that whatever rolethe exchange of ideas and technology may have played in the emergence of the Neolithic in theZagros, this was not accompanied with any substantial gene flow from other ancient Near EasternNeolithic centers of domestication.

Genetic continuum from Paleolithic to Neolithic Levant.

Among first farmers, those of the Levant trace ~2/3 of their ancestry to people related toNatufian hunter-gatherers and ~1/3 to people related to Anatolian farmers (Supplementary
Information, section 7).

[Fire Haired14]

Anatolia_Neolithic found a brother in Neolithic/Paleo Levant. Also, Neolithic/Paleo Levant clusters in West Eurasia exactly where we expected, just south of Anatolia_Neolithic by modern SouthWest Asians.

Huge Genetic shift in Chalolithic Anatolia.

Our about 6,000 year old genome from Western Turkey(same location as Neolithic Anatolians) is most similar to modern NorthWest Asians. So finally we have an answer as to when Turkey went from EEF to what it is today(for the most part).

[Fire Haired14]

In ADMIXTURE analysis....

>Anatolia Neolithic comes out as a mixture of Natufians and WHG/EHG.
>Armenia Chalolithic and Bronze, Anatolia Chalolithic, come out as Natufian+Iran Neo/CHG+WHG/EHG.
>Levant BA is Natufian+Iran Neo/CHG.

So all of this was expected. None of this is a surprise. For years now we've known "SouthWest Asian"(Natufian) and "Meditreaen"(Anatolia Neolithic) were closely related. We've also known that West Asians are a mixture of "SouthWest Asian" and "Caucasus"(CHG, Iran Neo).

This paper has supported another event we already knew. South Asian's West Eurasian ancestry is a mixture of Iran Neolithic and European/Steppe Bronze age.

[Angela]

I guess I'll call my friend and postpone that walk. :)

Where is Alan? He had it right about there being three farmer populations in the Near East, and without benefit of a leak from an about to be published paper.

I'll be back when I've read it carefully too, Bicicleur.

[LeBrok]

Wow, so many surprises! And it looks really rich in infor, and we have Natufians!!! I'm so excited, I'm skipping job today...., no, can't do that, lol. Cya guys later.
Lol, Natufians are E1b, my first guess before changing my mind to G2a based on EEF samples. Once again we have an example how Y DNA can shift quickly. But let's see where ENF genome comes from, maybe it is not Natufian but from Iranian farmer mostly. Later...

[Angela]

@Maleth,
It appears that the Natufians carry the precursor to E-M34. Thought you'd want to know. :)

[epoch]

In ADMIXTURE analysis....

>Anatolia Neolithic comes out as a mixture of Natufians and WHG/EHG.
>Armenia Chalolithic and Bronze, Anatolia Chalolithic, come out as Natufian+Iran Neo/CHG+WHG/EHG.
>Levant BA is Natufian+Iran Neo/CHG.

So all of this was expected. None of this is a surprise. For years now we've known "SouthWest Asian"(Natufian) and "Meditreaen"(Anatolia Neolithic) were closely related. We've also known that West Asians are a mixture of "SouthWest Asian" and "Caucasus"(CHG, Iran Neo).

This paper has supported another event we already knew. South Asian's West Eurasian ancestry is a mixture of Iran Neolithic and European/Steppe Bronze age.

Furthermore it confirms 25% ANE in WHG, ANE in Han. Although I have a tad problems with the numbers: They seem to change over the papers. Fu 2016 has slightly different numbers if I recall correctly: No ANE in Han or WHG due to no D-stat confirming it when Mal'ta is used.

And the three farmer populations was more or less already known from archaeology. The hotspots of the earliest neolithic transition were, according to archaeology: Zagros mountains, Catal Huyuk and the Levant.

EDIT: Fig. S11.3 models WHG as 7% ANE and 93% Bichon. Damn shame they didn't use the UP samples. Miss Fu worked at both papers, so I don't know exactly why. WHG proper is Loschbour?

[epoch]

More explained: Gedrosia is introduced from Iran to Steppe. Is also interesting to notice that the Caucasus has lot of the mentioned Y-DNA. Shame the paper has no mtDNA. I have a hunch there will be quite some updates.

EDIT: SI has no mtDNA, but supplementary data does. So I was lazy

[Angela]

For ease of reference:

Lazaridis Neolithic paper admixture chart.PNG

In this Admixture analysis, the Anatolia Neolithic appears to be a mix of Levant Neolithic, as defined as south Levant Neolithic (Jordan/Palestine), Iranian Neolithic, and some WHG.

By the time we get to the Anatolian Chalcolithic, or Copper Age, which some researchers call the Late Neolithic, we have an increase in the Iranian Neolithic, a bit of EHG, and a corresponding slight decrease in the WHG and Levant Neolithic. Yes?

How are we supposed to interpret this in light of the fact that the authors say these are genetically distinct populations? Is it partly a function of the time periods in question?

These are the dates provided in the paper itself for these samples:
"The samples include Epipaleolithic Natufian hunter-gatherers from Raqefet 125 Cave in the Levant (12,000-9,800 BCE); a likely Mesolithic individual from Hotu Cave in the 126 Alborz mountains of Iran (probable date of 9,100-8,600 BCE); Pre-Pottery Neolithic farmers 127 from ‘Ain Ghazal and Motza in the southern Levant (8,300-6,700 BCE); and early farmers 128 from Ganj Dareh in the Zagros mountains of western Iran (8,200-7,600 BCE). The samples 129 also include later Neolithic, Chalcolithic (~4,800-3,700 BCE), and Bronze Age (~3,350- 130 1,400 BCE) individuals.

I haven't gotten to the supplement yet. Does anyone know if all the Anatolian samples they used are from about 4800 BCE or later? If they are, there's a few thousand years for some admixture to have already occurred.

I'm not sure what to make of the Armenia Chalcolithic. Yes, they have some EHG and WHG, but so did the even earlier CHG hunter-gatherer. Indeed, so did the Iran_HotuIIIb sample. Then in the Early Bronze Age, the EHG decreases, probably as the result of further movement from the south, only for the EHG to increase again in the Middle Bronze Age.

Far from being a barrier to gene flow, the Caucasus range seems to have been remarkably porous. In that regard, perhaps some of this incoming EHG was by way of bride exchange between the Caucasus and steppe groups? So, no, I hate to dash anyone's fantasies, but probably not he-men steppe cowboys riding into the Caucasus to raid and steal wives.

Speaking of the steppe, this shows not only Iranian Neolithic genes on the steppe in the Early/Middle Bronze Age, but a bit of Levant Neolithic and WHG, which increases in the Middle/Late Bronze Age. So, did the latter two come with the people who came onto the steppe from the West Asian Highlands, or is it being picked up from people moving east from "Old Europe", since European EN here appears to be a three way mix of Iranian Neolithic, Levant Neolithic and WHG?

In Europe, the transition from the MiddleN/Chal to LN/Bronze sees the arrival of EHG, and a corresponding decrease in WHG and Levant Neolithic, but Iranian Neolithic stays the same.

I hate to be greedy when there is such a wealth of information here, but the only place from which we don't have farmer dna is precisely the area from which we know, or think we know, from the archaeology, that farmers set out for Cyprus, and, it was thought, other islands in the Aegean, and that is the area between southeast Anatolia and the northern Levant, approximately the area around northern Syria. I wonder if they would have been intermediate between northwest Anatolian farmers and Levant farmers?

This is probably why the authors are careful to say that there was no direct input from south Levant farmers into Europe. It was mediated by more northerly groups.

"To the west, the 270 early farmers of mainland Europe were descended from a population related to Neolithic northwestern Anatolians8 271 . This is consistent with an Anatolian origin of farming in Europe, 272 but does not reject other sources, since the spatial distribution of the Anatolian/European-like 273 farmer populations is unknown. We can rule out the hypothesis that European farmers stem directly from a population related to the ancient farmers of the southern Levant30,31 274 , however,"

@Epoch,
Maybe they were rushed because the paper had been leaked...

[epoch]

@Angela

Nah. I simply overlooked it. The Anatolians are Mathiesons, IIRC.

[Angela]

@Angela

Nah. I simply overlooked it.

No fair...you guys are six hours ahead. :)

[epoch]

No fair...you guys are six hours ahead. :)

The first issue I have: EHG is modeled as 25% WHG and 75% ANE (Being Afontova Gora2, they didn't use the far better genome of contemporary AG3). However in the admixture image you pasted above EHG is an element as well as WHG. Similar thing with SI table S7.25: Levant_N modeled as 1/3 Natufian and 2/3 Anatolia_N. Anatolia_N modeled as 0.4 Iran_N, 0.3 Levant_N, 1/4 WHG.

EDIT: Life isn't fair ;)

[Angela]

r

no G2a2 found, none
is G2a2 exclusive to Anatolian & European neolithic?

Yes, where was G2a2? Perhaps slightly further north at the intersection of the northern Levant and southeastern Anatolia? Is that the origin though or further east closer to the Iranian Neolithic given the "G" found there? (G2a1 is in the Iranian Neolithic and G1a in the Iranian Chalcolithic.)

I'm not sure Basal Eurasian originated in Africa though.
The reduced Neandertahl may be related to admixture with E-Z830 and unrelated to the Basal Eurasian.

I agree. I'm sure you've seen this by now:
", no 190 affinity of Natufians to sub-Saharan Africans is evident in our genome-wide analysis, as 191 present-day sub-Saharan Africans do not share more alleles with Natufians than with other 192 ancient Eurasians (Extended Data Table 1).
The idea of 194 Natufians as a vector for the movement of Basal Eurasian ancestry into the Near East is also 195 not supported by our data, as the Basal Eurasian ancestry in the Natufians (44±8%) is 196 consistent with stemming from the same population as that in the Neolithic and Mesolithic 197 populations of Iran, and is not greater than in those populations."

The latter is the point we made in our own speculations. Then you add in that they find no affinity in the Natufians to SSA populations. So, maybe those speculations of Dienekes' to the effect that there was an early back migration of "E" to Africa were correct?

So, as we also speculated, there was a refugia closer to the Persian Gulf? That or in North Africa?

While there was continuity from the Mesolithic to the Neolithic, there was no continuity from the Neolithic to the Chalcolithic. By that period at the latest, all these populations were mushed together, as we might have predicted from the archaeology.

"During subsequent millennia, the early farmer populations of the Near East expanded in all 253 directions and mixed, as we can only model populations of the Chalcolithic and subsequent 254 Bronze Age as having ancestry from two or more sources. The Chalcolithic people of western 255 Iran can be modelled as a mixture of the Neolithic people of western Iran, the Levant, and 256 Caucasus Hunter Gatherers (CHG), consistent with their position in the PCA (Fig. 1b).
Admixture from populations related to the Chalcolithic people of western Iran had a wide 258 impact, consistent with contributing ~44% of the ancestry of Levantine Bronze Age 259 populations in the south and ~33% of the ancestry of the Chalcolithic northwest Anatolians in 260 the west. Our analysis show that the ancient populations of the Chalcolithic Iran, Chalcolithic 261 Armenia, Bronze Age Armenia and Chalcolithic Anatolia were all composed of the same 262 ancestral components, albeit in slightly different proportions."

So, the Levant Neolithic people moved around, but at a certain point, there seems to have been a specific movement southwest from the northeast, so much so that this contributes 44% of the Levantine Bronze Age.

I wonder how close this population was to the ancient Hebrews?

[Angela]

As to the "Womb of Nations" idea, here is what they have to say:

"We computed squared allele frequency differentiation between all pairs of ancient West Eurasians29 216 (Methods; Fig. 3; Extended Data Fig. 3), and found that the populations at the 217 four corners of the quadrangle had differentiation of FST=0.08-0.15, comparable to the value 218 of 0.09-0.13 seen between present-day West Eurasians and East Asians (Han) 219 (Supplementary Data Table 3). In contrast, by the Bronze Age, genetic differentiation 220 between pairs of West Eurasian populations had reached its present-day low levels (Fig. 3): 221 today, FST is ≤0.025 for 95% of the pairs of West Eurasian populations and ≤0.046 for all 222 pairs. These results point to a demographic process that established high differentiation 223 across West Eurasia and then reduced this differentiation over time."

"
During subsequent millennia, the early farmer populations of the Near East expanded in all 253 directions and mixed, as we can only model populations of the Chalcolithic and subsequent 254 Bronze Age as having ancestry from two or more sources. "

"Admixture did not only occur within the Near East but extended towards Europe. To the 266 north, a population related to people of the Iran Chalcolithic contributed ~43% of the 267 ancestry of early Bronze Age populations of the steppe. The spread of Near Eastern ancestry into the Eurasian steppe was previously inferred7 268 without access to ancient samples, by hypothesizing a population related to present-day Armenians as a source7,8 269 . To the west, the 270 early farmers of mainland Europe were descended from a population related to Neolithic northwestern Anatolians."

[Angela]

The first issue I have: EHG is modeled as 25% WHG and 75% ANE (Being Afontova Gora2, they didn't use the far better genome of contemporary AG3). However in the admixture image you pasted above EHG is an element as well as WHG. Similar thing with SI table S7.25: Levant_N modeled as 1/3 Natufian and 2/3 Anatolia_N. Anatolia_N modeled as 0.4 Iran_N, 0.3 Levant_N, 1/4 WHG.

EDIT: Life isn't fair ;)

I know, Epoch, trust me. :)

That's what I was getting at partly...how "distinct" is distinct? It's going in a circle.

The "glue" or "tie" that binds is Basal Eurasian, yes?

O.K. I have to cook dinner, then dive into the Supplement, then I'll be back, by which time you guys will be asleep. A demain, then.

[Alan]

I guess I'll call my friend and postpone that walk. :)

Where is Alan? He had it right about there being three farmer populations in the Near East, and without benefit of a leak from an about to be published paper.

I'll be back when I've read it carefully too, Bicicleur.

thanks for mentioning me. :)

I remember Maciamo giving me a thumps up back than which means he agreed with this already back than.

I wrote allot of things in the other thread.

Here are my posts I wrote in the other thread.

HA I knew it I said it, but some people just jumped on wrong conclusions merely out of the fact that they don't like the idea of Yamna possibly being from Iranian Plateau.

Even the sentence "no direct geneflow" should have made anyone suspecious that they don't exclude indirect geneflow.


It makes archeological 100% sense. Maykop culture is descend of the Layla Tepe culture which according to archeologists derives from the Iranian Plateau.

I always said it

Iranian Plateau => Caucasus=> Steppes.

OR Eastern Iranian Plateau => Central Asia => Steppes.

From the paper Iran_N(Neolithic)
Iran_N

I1945: P1(xQ, R1b1a2, R1a1a1b1a1b, R1a1a1b1a3a, R1a1a1b2a2a)


So it seems there was R Haplogroup in Neolithic Iran. Take that all you haters ^^

Edit: I see the guys at Eurogenes are still in denial X)

The paper also perfectly proves my hypothesis that THREE distinct groups were living in the Near East at least by Neolithic.

A Southwestern farmer, A Anatolian farmer and a Iranian Plateau farmer/Herder group.

The Natufians were quite similar to Anatolian_Farmers but had some differences. And it seems that the Caucasian DNA in East Africa came via the Natufians rather than Anatolian_Farmers.

The Natufians were full of E1b1b and CT Haplogroups. Seems like we have found the source of the Egyptian culture in Levant_Neo. The whole Afro_asiatic family seems to be descend from the Levantine Neolithic.

Natufians and Anatolian farmers are very similar but still distinct, while Zagros farmers are significantly different from the former both.

Mesolithic Zagros H&G were more Basal Eurasian than Natufians which indicates that Basal Eurasian in fact derives from further East than South. Possibly Iranian coastle region.

And there seems to be EHG like ancestry in mesolithic Iran.

Mal'ta is modeled as ~28% Iranian Neolithic like, 15% CHG and ~35% WHG like

EHG is modeled as 80% WHG, 7% Iranian Neolithic and 10% CHG like.

[Alan]

Very nice new paper up. Dynamite: Natufians were only half Basal Eurasian and Basal Eurasian appears to have had no Neanderthal! Furthermore, the CHG part of Steppe appears to be made of Caucasian HG and part Iranian Chalcolithic. Fitted mixture proportions are 52.7% EHG, 18.1% CHG, 29.2% Iran_Ch.

Preprint: http://biorxiv.org/content/early/2016/06/16/059311
Supp Info: http://biorxiv.org/content/early/201...1.figures-only

The Neanderthal is very interesting as well. O, and Basal is not African. It is buried somewhere in the supp info tables.

EDIT: Y-DNA of Natufians were E1b and some J1. Iran G1a G2a and some J.

This could mean Basal Eurasian are the proto Eurasian who did not mix yet with Neanderthals. Natufians had E1b and CT as far as I remember. No known J1 among them.