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Friday, June 17, 2016

The genetic structure of the world's first farmers (Lazaridis et al. 2016 preprint)


Huge one from the Laz at bioRxiv:

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.

Lazaridis et al., The genetic structure of the world's first farmers, bioRxiv preprint, posted June 16, 2016, doi: http://dx.doi.org/10.1101/059311


And here's a list of the Y-chromosome haplogroups for the new samples in this paper:

Armenia_ChL (Chalcolithic Armenia)

I1407: L1a
I1632: L1a
I1634: L1a

Armenia_EBA

I1635: R1b1-M415(xM269)

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)

Update 25/07/2016: The peer-reviewed paper was published at Nature today under the title Genomic insights into the origin of farming in the ancient Near East. See here.

See also...

A moment of clarity

Early Neolithic genomes from the eastern Fertile Crescent (Broushaki et al. 2016)

349 comments:

1 – 200 of 349   Newer›   Newest»
Rob said...

This is Epic
Solves a lot of questions

Davidski said...

It is epic, although I'm not sure it solves most things yet.

But at least my estimates of steppe ancestry in South Asia were generally pretty solid.

Rob said...

Yeah Dave. Virtually spot on

Rob said...

Its actually bigger than I imagined.

Davidski said...

It's big.

Jijnasu said...

Can we finally bury the OIT now?

Davidski said...

Of course we can. It's dead and buried.

Karl_K said...

This is an incredibly interesting paper.

Gioiello said...

Very likely this is also the definite proof of my Italian Refugium of R1b1 (and I hope also of R1a) and much other. Someone says to some Ulixides that hg. J has nothing to do with Middle East, but arrived there not before 5000 years ago from Caucasus very likely (and that Italy and Europe have subclades long before Middle East). No surprise to me about Natufians.

Labayu said...

Craniometric analyses have suggested that the Natufians may have migrated from north or sub-Saharan Africa 25,26 186, a result that finds some support from Y chromosome analysis which shows that the Natufians and successor Levantine Neolithic populations carried haplogroup E, of likely ultimate African origin, which has not been detected in other ancient males from West Eurasia (Supplementary Information, section 6) 7, 8, 189. However, no affinity of Natufians to sub-Saharan Africans is evident in our genome-wide analysis, as present-day sub-Saharan Africans do not share more alleles with Natufians than with other ancient Eurasians (Extended Data Table 1).

Seems the migration could have easily gone the other direction.

From Poznik et al 2016:

Consistent with previous proposals 14, a parsimonious interpretation of the phylogeny is that the predominant African haplogroup, haplogroup E, arose outside the continent. This model of geographical segregation within the CT clade requires just one continental haplogroup exchange (E to Africa), rather than three (D, C, and F out of Africa). Furthermore, the timing of this putative return to Africa—between the emergence of haplogroup E and its differentiation within Africa by 58 kya—is consistent with proposals, based on non–Y chromosome data, of abundant gene flow between Africa and nearby regions of Asia 50–80 kya15.

http://www.nature.com/ng/journal/v48/n6/full/ng.3559.html

Karl_K said...

The tests with the Mota sample surprised me. The authors don't say too much, but if Mota actually had zero admixture at all from any of these Basal Eurasian or farming populations, that says something.

I think it is likely that there were much earlier 'back migrations' from the Basal Eurasian population to Africa. But without an actual ancient sample, they can't really say anything. The ghost population can work in some contexts, but I don't think it works when looking at back migrations to Africa from a Eurasian population.

Karl_K said...

@Gioiello

"Very likely this is also the definite proof of my Italian Refugium of R1b1 (and I hope also of R1a) and much other."

Finally. Someone has had the guts to speak the obvious truth. I applaud the authors of this paper for following through with the dream of proving these hypotheses.

Could you just point me to the part where they show the proof if it? I think I may have overlooked it in my haste.

Gioiello said...

"To the west, the early farmers of mainland Europe were descended from a population related to Neolithic northwestern Anatolians. This is consistent with an Anatolian origin of farming in Europe, but does not reject other sources, since the spatial distribution of the Anatolian/European-like farmer populations is unknown [p. 8].
"We can rule out the hypothesis that European farmers stem directly from a population related to the ancient farmers of the southern Levant, however, since they share more allele with Anatolian Neolithic farmers than with Levantine farmers as attested by the positive statistic f4(Europe_EN, Chimp; Anatolia_N, Levant_N) (Z=15) [pp- 8-9].
"Previously, the West Eurasian population known to be the best proxy for this ancestry was present-day Sardinians, who resemble Neolithic Europeans genetically. However, our analysis shows that East African ancestry is significantly better modelled by Levantine early farmers than by Anatolian or early European farmers, implying that the spread of this ancestry to East Africa was not from the same group that spread Near Eastern ancestry into Europe (Extended 283 Data Fig. 4; Supplementary Information, section 8)" [p. 9].
"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 ‘Indian Cline’ of such ancestry is inferred to have ~18% steppe-related ancestry, while the Kalash of Pakistan are inferred to have ~50%, similar to present-day northern Europeans".
"Northwest Anatolians—with ancestry from a population related to European hunter-gatherers (Supplementary Information, section 7)—are better modelled if this ancestry is taken as more extreme than Bichon (Supplementary Information, section 10)" [p. 10].

But Levantinists and Stanford's Leftists persist: "The population structure of the ancient Near East was not independent of that of Europe (Supplementary Information, section 4), as evidenced by the highly significant (Z=-8.9) statistic f4(Iran_N, Natufian;WHG, EHG) which suggests gene flow in ‘northeastern’ (Neolithic Iran/EHG) and ‘southwestern’ (Levant/WHG) interaction spheres (Fig. 4d). This interdependence of the ancestry of Europe and the Near East may have been mediated by unsampled geographically intermediate populations that contribute ancestry to both regions" [p.10].


Karl_K said...

@Gioiello

I didn't see where they mention R1 haplogroups in all that.

Gioiello said...

@ Karl_K
"Could you just point me to the part where they show the proof if it? I think I may have overlooked it in my haste."

Have you looked at some R1b1 or R1a1 in aDNA from there? I remember to you Villabruna, Belluno, Italy, 14000 YBP R1b1a* and I am sure that they will find also R1a...

Davidski said...

I'm going to try and challenge some of the findings in this paper when the data is released.

But it's a very nice effort all round, and I'm pretty happy that it's now basically certain that R1a-M417 expanded from Eastern Europe both into Central Europe and Asia.

Alberto said...

This is huge. It will take some time to read and digest, but can't wait for all to get their heads around it and start dissecting it :)

How long does it usually take for the data to become available after this pre-prints?

George Okromchedlishvili said...

1. Super interested in Neolithic Iranian sample. This guys seems close to South Caucasian G2a

2. I was right in expecting Natufians (and prob Basal Eurasians as well) to be E1b.

3.There was A LOT of turnover in the Middle East pops

Krefter said...

The mtDNA results were all expected. 99.9% of West Eurasian mtDNA that isn't U(xK, U1, U3, U7, U9) is Middle Eastern. No more pet-theories about loads of mtDNA H hiding in some Paleolithic gravesite in Spain.

Unlike Anatolia_Neolithic, the new Neolithic Middle Eastern mtDNAs don't belong to European-specific subclades. N1b, R0a(inclu. R0a2), T1a2, and H14a in Neolithic Levant are all most typical of modern Levant/SouthWest Asia today.

U7a appeared in Neolithic Iran and is today most popular in Iran(and also has a strong presence in South Asia). U3a has been found in Neolithic Iran, Neolithic Anatolia, and Chalothic Armenia and is today most typical of West Asia(specifcally Levant) but also has presence in Europe.

Important small details about mtDNA links between Chalolithic Iran/Aremenia and Bronze age Europe that didn't exist in Europe during Neolithic. It's been obvious these are CHG lineages for a while and now we have good confirmation.

>mtDNA I1(specf. I1c)
>T1a1'3
>H2a1: Also appeared in Chalolithic Samara Russia. No doubt a CHG lineage.

Also mtDNA U4a, typical of EHG, was in one of the Chalolithic Armenians.

Iranocentrist said...

"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."

Iran is the source of IE, there you have it

Karl_K said...

@Gioiello

"I am sure that they will find also R1a..."

Sure they will. But so far, that isn't exactly what people call 'proof'.

Rob said...

Sam/ Krefter

"Important small details about mtDNA links between Chalolithic Iran/Aremenia and Bronze age Europe that didn't exist in Europe during Neolithic. It's been obvious these are CHG lineages for a while and now we have good confirmation. "

Ah ok
It's good we can now see what we couldn't yesterday
;)

Davidski said...

@Iranocentrist

Iran is the source of IE, there you have it.

No it's not. Not even Indo-Iranian languages are from Iran.

You're ignoring the part where they say "related to". The genetic structure in Iran changes from the Neolithic to the Chalcolithic, so Iran wasn't the source of the Iranian-like admixture on the steppe.

Also, unless women spread Indo-European languages onto the steppe, then the population that migrated both to the steppe and Chalcolithic Iran wasn't Indo-European. That's because there are no Y-HG J or G in any elite Kurgans, not even in one.

Karl_K said...

@Davidski

"Also, unless women spread Indo-European languages onto the steppe, then the population that migrated both to the steppe and Chalcolithic Iran wasn't Indo-European."

This you actually do not know. It could have been the case, no matter how unlikely in your mind that women could spread language.

Rob said...

I agree Karl
We now know that women moved around more than men, right, along with sheep and metals (although far more valuable) ?

Rob said...

"That's because there are no Y-HG J or G in any elite Kurgans, not even in one."

The steppe kurgans are just burial grounds of family men. They're not really "elites". Even women are found in kurgans

Krefter said...

@Davidski,

CHG admixture didn't enter Yamnaya via a female market stretching 100s of miles. That's impossible considering they barely had wheels and horses. A large percentage, maybe as many as women, of Yamnaya's CHG ancestors were men. It looks like admixture was sex bias but it wasn't as sex bias as Y DNA would suggest.

Nirjhar007 said...

So its R1b1?

Krefter said...

No one predicted that 8,000 years ago R1b/a were the primary haplogroups in Russia, while J(2?) and L1a dominated Iran and G2a2 dominated Turkey. Instead Iran and Turkey were thought to be the source of modern R1a/b. Papers based on Y DNA were wrong because often modern mtDNA can't tell us anything about the distant origins of haplogroups.

Nirjhar007 said...

Its P* .

Krefter said...

It's P1. It wasn't able to be tested for many P1 subclades, so all we know is that it's P1. Definitely R in my opinion.

Hrvoje said...

So, proto-Afro-Asiatic was a Neolithic Levantine language after all. Also, Afro-Asiatic was not present in Europe until the Phoenician colonization.

Davidski said...

It's probably R2. Note also the L in Chalcolithic Armenia.

Think about it. South Asians have a lot of R2, and they have a lot of Neolithic Iranian ancestry.

We might be able to check when the bam files are released.

Davidski said...

@Rob

The steppe kurgans are just burial grounds of family men. They're not really "elites". Even women are found in kurgans.

So the R1a/R1b men buried with weapons and sacrificial offerings, even human in many cases, were not elites?

Come on.

Hector said...

The reactions are just as entertaining as the article is informative.

Davidski said...

@Hector

You are the comedian here.

Rob said...

It seems there was virtually no ANE in Iran before the Bronze Age ?
Only 1% ANE admixture in the Hotu Cave sample
But ~ 14% by Copper Age Iran

Today its much lower, isn;t it ?

Nirjhar007 said...

p.57

First, the Mesolithic individual from Iran belonged to haplogroup J. This has also been
detected in two hunter-gatherers from the Upper Paleolithic in Georgia11, as well as in a
hunter-gatherer from Karelia in northwest Russia5
, suggesting that it had a widespread early
distribution prior to the spread of farming with which its current distribution was initially
associated12. While the hunter-gatherers from Georgia resemble the one from Iran (Fig. 1b),
their whole genome data shows very different patterns from the Eastern European huntergatherer
who also possessed this haplogroup, as well as from a singleton Anatolian early
farmer who belonged to haplogroup J2a5
. This should serve as a note of caution against the
idea that Y-chromosome lineages can be thought as markers of populations and population
movements

Nirjhar007 said...

"While the Early/Middle Bronze Age ‘Yamnaya’-related group (Steppe_EMBA) is a good genetic
match (together with Neolithic Iran) for ANI, the later Middle/Late Bronze Age steppe population
(Steppe_MLBA) is not."

Nirjhar007 said...

Movements to India and Europe by 3000 BC , probably starting around 3800 BC.

Davidski said...

From Eastern Europe.

Rob said...

Dave

"So the R1a/R1b men buried with weapons and sacrificial offerings, even human in many cases, were not elites"

Which R1a/ R1b men are you talking about specifically.? There are many such people.
If you are referring to Yamnaya : then not many at all, actually. Some ochre, temple rings, few had wagons, but mostly those in or near Majkop. The latter of which certainly ha chiefly kurgans with lost of weapons and metal.

If you're talking about CWC, then yes. But it's all very Copper Age Europe stuff: axes, arrows, etc.

Sitashta: yes , quite significantly. But that's like 2000 BC. By then, high quality weapons and elites are found throughout Eurasia - Germany, Carpathian basin & Balkans, Anatolia, Greece, etc

Nirjhar007 said...

From Eastern Europe.

heh, let the Indian and Stans aDNA come up first...

PF said...

Guess the answer to my question when Natufian DNA is coming was: tomorrow!!!

Still a bit unclear exactly how close the E1b1 Levantines are to the G2a Anatolians. It looks like they're on opposing sides of a still quite tight cluster, while the Zagros farmers are distinct. Admittedly I expected G2a in the Levantines, though I guess it could still pop-up in contemporaneous sites nearby, perhaps on the coast.

I want to see which modern populations fall between them on the otherwise empty part of the PCA they allude to, though of course it is obvious! One of the clearest PCAs by the way, where everything is nice and square and just "makes sense."

Karl_K said...

@Nirjhar

". This should serve as a note of caution against the idea that Y-chromosome lineages can be thought as markers of populations and population movements"

But you need to be aware of the differences in timespan and number of mutations for each specific case.

A very minor number of mutations in a short time is likely an indication of a direct population movement.

Hector said...

There are numerous cases where the language of the females becomes dominant eventually. English is the best example against both the Scandinavian males and French speaking Normans.

But in almost all such cases females are resident natives. It is very rare that migrating females carry the language in the patriarchy-dominated Eurasian continent.

In the case of Polynesians the language appears more closely related to the females. But their male counterparts are not entirely absent. In fact in some Polynesian islands O's are the majority instead of C1b.

But Kurgan burials may preserve the dead better than other forms. The most notable practice in the steppe is an open burial where the dead are left on open(usually high) grounds. Cremation is another. The latter two obviously preserve the remains less well. Kurgan remains may not faithfully represent the population under investigation.

Gioiello said...

@ Krefter

"The mtDNA results were all expected. 99.9% of West Eurasian mtDNA that isn't U(xK, U1, U3, U7, U9) is Middle Eastern. No more pet-theories about loads of mtDNA H hiding in some Paleolithic gravesite in Spain".

Let's wait. I wrote about mt in Europe and Italy even more than about the Y. I'll study those haplotypes, but be warning that these theories of some friends of yours end up as their theories about Y R1b from Middle East!

Nirjhar007 said...

Karl,

The paper accepted, what I was saying for long time, autosomes and SNP's don't have any direct relation!....

Davidski said...

@Nirjhar007

heh, let the Indian and Stans aDNA come up first...

Like I told you ages ago, South Asians have Eastern European steppe ancestry. It's now finally confirmed with this paper.

mickeydodds1 said...

With reference to the putative 'North Iranian R1s', 'it's squeaky bum time', in the immortal words of Sir Alex Ferguson.

Nirjhar007 said...

Its not confirmed . The common ancestry is confirmed. To know from where it came , we need aDNA from SC Asia. Also to know how archaic it is...

Davidski said...

@Hector

You need to use all of the available information.

So ask yourself: what are the lineages in the elite Middle/Late Bronze steppe Kurgans, and what lineages did really well in South Asia during the Bronze/Iron Age based on modern DNA?

Can you give us the answer? And does the ancient DNA contradict the modern DNA, or not?

Thanks in advance.

mickeydodds1 said...

Does this put to an end, once and for all, the endless debating of whether y DNA haplotype E1 is ultimately African or Eurasian in provenance?

Davidski said...

@Nirjhar007

Your hopes and dreams are based on the assumption that Central Asia was populated by almost identical Yamnaya-like populations as Eastern Europe, with loads of EASTERN EUROPEAN HUNTER-GATHERER ancestry.

There's no chance of that. You know why? Because Central Asia is not Eastern Europe.

Rami said...

Those Steppe EMBA for lot of those South Asian groups are greatly inflated lol and more related to Yamnaya than the Indo Iranian steppe hmm. Mala with 20% steppe ancestry , come on now lol. As per the paper EHG is defined as a mix of WHG and a population on the Onge/Han cline. They really need genomes from Central/South Asia to explain away the high levels of ANE there, because the Zagros Farmer is mostly Basal.

PF said...

It's early in the morning and I haven't had coffee yet... They're saying that the Zagros samples are a better proxy than CHG for the non-EHG portion of Steppe, right?

Karl_K said...

@Davidski

Didn't you hear?

"autosomes and SNP's don't have any direct relation!...."

Try and wrap your head around that one.

Davidski said...

Mala has 18% Steppe_EMBA, so there.

And if we assume that the Indo-Aryans who moved to South Asia were BMAC + Andronovo, the stats change.

So yeah, wait for BMAC data, but don't expect the steppe contribution in South Asia to be small by any stretch.

Krefter said...

CHG/Iran Neolithic-related admixture in Chalolithic Anatolia+Levant and Early Bronze age Armenia.
EHG/Steppe admixture in Late Bronze age Armenia.

Rami said...

Nirjar has a point David, why are Yamnaya people are far better fit than your beloved Androvono . The fact Yamnaya is mainly Iranian derived, is a big hint.

Davidski said...

@PF

It's early in the morning and I haven't had coffee yet... They're saying that the Zagros samples are a better proxy than CHG for the non-EHG portion of Steppe, right?

Nope.

They're saying Iran Chalcolithic is a better proxy for non-EHG in Yamnaya. And Iran Chalcolithic is very different from the early Neolithic Zagros farmers.

But what they also say in the supp info (page 83) is that Yamnaya can be modeled as EHG, CHG and minor Near Eastern.

However, what they don't consider is that Yamnaya might actually be EHG, CHG and CT. And I reckon this is what Yamnaya really is.

Rob said...

oK. Lets go to first base. Im trying to understand the Near East deal.

The first issue is the correlation of Basal Eurasian, no Neanderthal admixture, and trying to piece that into what we thought - AMHs first encountered Nanderthals exactly in the Near East.

So it means that BE came from somewhere further south, after the LGM. But it had no signs of sub-saharan admixture, and is not earlier or more basal in the Levant than Iran. Given that there is clear attestation of a recent back-migration into Africa from a south Levantine population, it seems likely that the Basal Eurasian came from a refuge somewhere near the Persian Gulf.

Again, the lack of ANE in Mesolithic Iran must mean that wherever ANE came from, it wasn;t too close to the Zagros.

Nirjhar007 said...

David,

Its almost certain now that, there were movements from SC Asia to India and E Europe .

Your CHG wife theory is also dead . Neolithic movements from Iran to Europe did happen! .

We can assume there were y-dna associated with it. But we need y-dna evidence still.

Karl_K said...

@Rob

"Given that there is clear attestation of a recent back-migration into Africa from a south Levantine population"

True that there was a back migrations, but it could have been a back and forth for a long time.

There are not enough samples to say much at all.

Various Basal Eurasian lineages could have been all over North Africa until say, 20,000-15,000 years ago. After that time, SSA groups could have migrated in, only to be again largely replaced by a Eurasian back-migration. And then a Neolithic migration moved in as well.

There is just no way to know at this point.

Davidski said...

@Rami

Nirjar has a point David, why are Yamnaya people are far better fit than your beloved Androvono . The fact Yamnaya is mainly Iranian derived, is a big hint.

One thing you should burn into your brain: Nirjhar never has a point.

BMAC + Andronovo might be an even better fit than Yamnaya.

And anyway, Yamnaya is not mainly Iranian derived, unless you pretend that the Caucasus and its hunter-gatherers didn't exist. But wait, oops, they did.

And R1a-Z93 is a Bronze Age steppe marker, not from Iran. Oops again.

Davidski said...

@Nirjhar

Its almost certain now that, there were movements from SC Asia to E Europe.

lol

Davidski said...

@Rob

As is Copper Age Iran is mimicking CT?
How?


EHG + CHG + minor Near Eastern (see supp info page 83) is mimicking EHG + CHG + CT.

They didn't consider this.

Karl_K said...

@Davidski

But don't they also show that Caucasus hunter-gatherers (CHG) could be a mixture of Iran_N and both WHG and EHG?

(Extended Data Figure 6: Admixture from ghost populations)

Rami said...

For upper caste NW South Asians , I am sure there will be a substantial amount of Indo Iranian steppe admixture BUT , if you look at groups like Mala, Baloch ,Brahui with 20-33% , that is illogical for them to have that much Indo-Iranian admix , that "steppe" like ancestry is coming from else where.

Karl_K said...

@Nirjhar

"Its almost certain now that, there were movements from SC Asia to E Europe."

This is a very interesting usage of the word 'almost'.

Nirjhar007 said...

''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
.''

Rob said...

@ Karl

"True that there was a back migrations, but it could have been a back and forth for a long time.

There are not enough samples to say much at all.

Various Basal Eurasian lineages could have been all over North Africa until say, 20,000-15,000 years ago. After that time, SSA groups could have migrated in, only to be again largely replaced by a Eurasian back-migration. And then a Neolithic migration moved in as well.

There is just no way to know at this point."


Yes, im not pretending to know what occurred in northern Africa over the eons, but rather the B.E. in Neolithic Europe & the Near East. If Iran Neolithic & Levant Neolithic are equidistant to it, then it probably came from between the two, rather than from one to the other.
Or is that too simple ?

Davidski said...

@Nirjhar

There's nothing at all in this paper that suggests there were population movements from SC Asia to Eastern Europe.

Nothing at all.

Hector said...

@davidsky
It would be more convincing if the remains from accidental deaths also yielded mostly R1a/R1b males.

Typical patrilineal societies exchange females between tribes while male lines are preserved(the very definition of 'patrilineal'). If one is buried in kurgan style while the other practiced cremation, archaeologists will only find the ones from kurgans, and someone like you will jubilate. "Aha I only see 'European' male lines while some of the female lines are from ***."

But in fact the tribe that practiced cremation had exactly the opposite pattern. Their male lines are almost entirely *** while some female lines are of European origins.

All modern populations are results of admixture. Even if South Asians are patrilineally European partially, that does not mean they are any more hybrids or are more illegitimate than Eastern Europeans who are also results of admixture in different patterns.

Krefter said...

@mickeydodds,
"Does this put to an end, once and for all, the endless debating of whether y DNA haplotype E1 is ultimately African or Eurasian in provenance?"

These Neolithic Levant guys specifically appeared to have had E1b-M123 not a basal form of E. E1b-M123 existing in the Levant in 10,000 BC is as good evidence E originated in Eurasia as E1b-M123 existing in the Levant in 2000 AD.

We need older samples, from Africa and Eurasia, because E is over 50,000 years old. There's a little known study with 6,000 year old Y DNA from Sudan which is mostly DE(not tested for E).

Karl_K said...

@Rob

"Or is that too simple ?"

I would say that judging by what we know about places with much better sampling, then it is way too simple.

We know nothing about any of this region before 12,000 years ago other than there were many populations that were highly structured and diverse.

Rob said...

@ Karl

"But don't they also show that Caucasus hunter-gatherers (CHG) could be a mixture of Iran_N and both WHG and EHG?"

Its quite funny.
They have Iran Neolithic -> CHG (~ 60%)
Then CHG -> Iran Chalcolithic (60%)

Like a circle
Does it mean that by the Chalcolithic, the two regions had fused ?

Nirjhar007 said...

So... two main points :

1. 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.

2. While the Early/Middle Bronze Age ‘Yamnaya’-related group (Steppe_EMBA) is a good genetic
match (together with Neolithic Iran) for ANI, the later Middle/Late Bronze Age steppe population
(Steppe_MLBA) is not.

They suggest that the Steppe like ancestry came to India from the Steppes in bronze age , But ANI is clearly older than any such date, its now clearly indicated. They say it ONLY because they assume such ''steppe like'' ancestry did not exist in S Asia before bronze age. Its going to be proven that such ancestry was present in SC Asia , and population from that area migrated both to India and Europe!.

Karl_K said...

@Rob

It just means that they need more samples. A lot of the language in this paper (and that new Native American overview paper) are making it clear that there is often more than one way to analyze genetic data.

The authors know that they could be wrong, so they use language to reflect the uncertainty.

In the case of the circular ancestry, they need older samples to decide which is correct.

Davidski said...

@Hector

Quit talking out of your ass and answer this question.

Do the Y-haplogroups in the elite Middle/Late Kurgans match the Y-haplogroups that have experienced massive founder effects dated to ~4,000 YBP in upper caste South Asian populations?

Yes, no, maybe?

Karl_K said...

@Nirjhar

"They say it ONLY because they assume such ''steppe like'' ancestry did not exist in S Asia before bronze age."

That is just crazy. Just because all of the data that they actually have suggests this, they keep assuming that their data reflects some actual history. Have you sent them your email address? Maybe they are unaware of all the data you have been collecting independently.

Karl_K said...

@Hector

"Do the Y-haplogroups in the elite Middle/Late Kurgans match the Y-haplogroups that have experienced massive founder effects dated to ~4,000 YBP in upper caste South Asian populations?

Yes, no, maybe?"

I think the answer is yes. Which would be a pretty amazing coincidence if these were burials with no significance amazing to all.

Rob said...

@ Matt


When you get the cnance, can you do one of your PCAs, with the WHG- Levant farmers sitting on a N- S axis. ?

Rob said...

@ Karl

"I would say that judging by what we know about places with much better sampling, then it is way too simple."

Maybe too simple, but Im not often wrong.

That we see the most basal lineage is the Iran Mesolithic instead of (the even older) Natufian is clear cut: BE cannot have come from northern Africa directly. But somewhere surprisingly further east, well inland in western Asia.

PF said...

@Rob

It may or not be too simple, but there's been a lot of evidence that Basal formed, or at least expanded from, the Gulf area. A recent case that makes a good claim based on R0a2: Mapping human dispersals into the Horn of Africa from Arabian Ice Age refugia using mitogenomes http://www.nature.com/articles/srep25472

To get really spacey, it's possible that Basal descends literally *from* the Gulf, before it was flooded. That would explain similar flood myths that arise across otherwise disparate but Basal-rich areas.

Krefter said...

This paper didn't even investiagte very much the relationship between ancient and modern genomes. I don't blame them at all. But anyways here are some specualtions about the modern affinities of Natufians

Everything from this paper was 100% expected. Natufians in my opinion will turn out to be the primary ancestors of SouthWest Asians and North Africans. I see evidence of this in mtDNA/Y DNA not just PCA, F4-stats, etc. However Sardinians are probably their closest living relatives, because of African admixture in SouthWest Asia/North Africa.

Natufians and Neolithic Turkey are closely related. Natufians are not ancestral, at least to a large degree, to Neolithic Turkey though. They're just close relatives. This is SouthWest Asians, like Bedouin, have been modeled successfully EEF.

I wouldn't be surprised if Natufians were Afro Semetic speakers because everyone who speaks a Afro Semetic language has loads of Natufian-related ancestry(including Eastern Africans).

Hector said...

@davidsky

I envy your ability to be proud of someone else's ancestors.
The putative origin of R1a1 even in your scenario was not Slavic even 1500 years ago.

Jijnasu said...

As regards their comment on the ANI ancestry of South Asians, is it possible that they descend from the inhabitants poltavka and Andronovo represents an extinct related population? Andronovo appears rather late to be an ancestral settlement to the indo-aryans

Rob said...

@ Dave


"However, what they don't consider is that Yamnaya might actually be EHG, CHG and CT. And I reckon this is what Yamnaya really is."

yes,
The paper states that Yamnaya can be modelled also as 3 way mix between EHG, CHG and ANF. This ANF could have come from CT

Karl_K said...

Come on Krefter. We all you that you are omnipresent, but even you did not expect >99.9% of this paper.

They didn't go into comparison with modern populations because these authors tend to get 3 or 4 major publications out of each new data set. It is good for their funding, which is good for the rest of us. (No matter how screwed up the funding system is).

Nirjhar007 said...

Karl ,

They say early bronze age steppe folks and ANI have close affinity . They say that late BA steppe folks don't have such affinity ! . They concur that by getting aDNA from ''South of Steppes'' will resolve the issue !.

That's what it is.

Getting the aDNA from SC Asia , then we can talk about data concluding the things.

Rob said...

With all this extra data, it also proves beyond doubt that Sintashta-Andronovo is from eastern Europe, given that it is steppe with distinctly European middle Neolithic, nor Levant, Anatolian or Iranian.

Karl_K said...

@Hector

"The putative origin of R1a1 even in your scenario was not Slavic even 1500 years ago."

Most of the people who's bones were drilled into in this study were ay least a bit related to ancestors of most of the people who read this blog.

I think we all have a right to call them 'our ancestors', whether or not Slavs existed in their time. (And I don't have any obvious Slavic ancestry if you are wondering).

Karl_K said...

@Nirjhar

"That's what it is."

So let's go get it!

But I hope you are just having a laugh, because... you know...

Davidski said...

@Jijnasu

I discussed the problem of the current Andronovo and Sintashta samples not being very good references for steppe admixture in South Asia in my Srubnaya outlier post.

http://eurogenes.blogspot.com.au/2016/04/the-srubnaya-outlier.html

Basically, it seems that Z93 and Indo-Iranian languages spread from the Ural steppe with a population with a higher ANE ratio than the Andronovo and Sintashta samples we currently have. This population may have been very similar to one of the samples in the Srubnaya sample set.

Mix guys like this with BMAC farmers, and voila.

@Hector

You've completely lost me with the Slavic angle.

MfA said...

Levant Bronze Age (J and J1) seems like basically Levant_N + Iran_Chalcolithic

http://abload.de/img/asdbzl0z.png


Iran_ChL

13,4 EHG
62,3 Iran_N
20,0 Levant_N
4,3 WHG


Levant_BA = 56% Levant_N + 44% Iran_ChL


5,9 EHG
27,4 Iran_N
64,8 Levant_N
1,9 WHG

Krefter said...

@Karl_K,
"Come on Krefter. We all you that you are omnipresent, but even you did not expect >99.9% of this paper."

Yes I am omnipresent and knew what the results would be because, yesterday I was hanging out with my Natufian and Zagros pals, that's how I knew what the results. I'm their Fire God.

No actually coincidentally yesterday I visited the Oriental Institute at Chicago University yesterday. It's a world-class museum on the ancient Middle East and includes a lot of artifacts from the Paleolithic and Neolithic.



Chad Rohlfsen said...

I think we'll see confirmation that CHG/ Zagros is in Anatolians, but more Natufian to Anatolian in Spain. It was fairly easy to put CHG in LBK and Hungary before this and it should be easier now. Hopefully, the data is released soon.

Seinundzeit said...

Wow, don't even know where to begin!

I'm leaving for work in a moment, so I can't say much. I'll read this thing in detail much later (so much to digest). Anyway, I can't believe so many questions just got answered in this paper, tremendous stuff.

But just to get it out there, finally, it's good to see that the whole debate concerning the LN/EBA European genetic contribution to Central Asia/South Asia is finally over. The Kalash are 50% something very similar to Northern Europeans (and Pashtuns are fairly similar), in the words of this paper. It's funny looking back, at how contested this was.

In addition, it seems my notion concerning Balochistan was correct, but I had the wrong Baloch populations in mind. It seems Makranis (who are really coastal Baloch. Makrani is a confusing label, also applied to Balochi-speakers of predominantly African descent) are pretty much overwhelmingly Iranian Neolithic, although I'm sure there are more inland Baloch tribes who can also be construed as such. There is going to be genetic structure in such a tribal region.

Hector said...

Qiaomei Fu working with Paabo reported to have typed Tianyuan sample's Y chromosome according to a Chinese guy at ranhaer or something. That was last year.

It may be a fraud.

"Dear ***,Thanks for interested in our work. The Y chromosome results will also show in the paper. Since the paper will come out soon, you will now all the details.
Best,
Qiaomei"

Fu's English cannot be that bad in my opinion. I think the Chinese guy made it up.

Anyway whatever the result is, you can bet that davidsky will claim a victory of some sort. I have never seen him admit he erred.

Rob said...

For South Asian admixture, they're pretty clear that the ANI is Iranian Neolithic + some steppe. It's curious & probably significant that South Asians are modelled as Neolithic Iran, rather than Chalcolithic Iran. If correct, then it means that Iran_Neolithic was probably present in South Asian already since the Neolithic, and the only "new" component is from the steppe? (albeit potentially carrying Chalcolithic Iran stuff)

Nirjhar007 said...

So Rob,

They mean ANE came from the steppes directly with ''IE''s?.

Nirjhar007 said...

There is still a scientific possibility that, that P* will be of R1 clade!

Shaikorth said...

Here's something odd about those Natufians, while waiting for further testing.

Fst(Natufian-Mbuti)/Fst(Natufian-Papuan) = 0.9522
Fst(BedouinA-Mbuti)/Fst(BedouinA-Papuan) = 0.9778
Fst(BedouinB-Mbuti)/Fst(BedouinB-Papuan) = 0.9901

This statistic is 1 or more for non-Africans without African, and even some with a little of it like Jordanians. It is also >1 for Iranian Neolithic who have less Neanderthal admixture and more "basal" according to the paper, in fact it's almost identical for Iranian and Anatolian Neolithics..

Gioiello said...

@ Karl_K
"@Gioiello

"I am sure that they will find also R1a..."

Sure they will. But so far, that isn't exactly what people call 'proof'".

Perhaps you misunderstood me: I did mean in Italy, not in Middle East!

Rami said...

The Chl Iranians are probably why there is inflated steppe ancestry in lot of those South Asian groups. Once the Genomes of those Rakhigarhi samples are out, that will explain that well. Now I am starting to think the BMAC was populated by Chl Iranians, which would make sense as proto BMAC was derived from cultures along the Caspian.

Nirjhar007 said...

Possible, with decent amount of R1a-Z94 and some J2 also...

Matt said...

Wow. You guys. So huge.

Just noticed this existed basically 30-45 minutes ago. So many answers will be in this.

Initial reactions:

The huge implication is that we now know we have at least two "Neolithic Dawns" in West Eurasia, initially apparently genetically separated.

More work will be needed (and hopefully there are fossils) to learn if these were truly totally genetically separated, or whether the Levant Neolithic and Iranian Neolithic involved some degree of genetic exchange (by populations yet more isolated than the Neolithic Levant and Iranian here).

We also see now that the south of West Eurasia was also beginning to merge, during the Bronze Age, in the same way as the north of West Eurasia. There is a broader dynamic here

However, before I get down to reading for anyone who has read and understood, do these big questions remain?:

- Did the Natufians or Levantine Neolithic populations contribute to the Anatolian Neolithic at the right time frame, or were they a separate population? I.e. were the Levantine farmers bringers of the Neolithic to Anatolia, or were they a structured population that developed it at the same time, using trade, like the Neolithic Levant and Iran are).

(If so, it looks at least from their ADMIXTURE like after the Levant Neolithic populations are considered, the ultimate "genetic survival" by the broader WHG-Villabruna clade may be much more comparable to EHG than we thought! Although the contribution by the West European members of the clade would still be low.)

(Another aside, the pattern of the position of BedouinB on that PCA makes you wonder what will happen if with ever get Neolithic Arabian dna. Though with this paper that's not an *if* anymore, it's a *when*).

- Just from PCA Chalcolithic Armenia perfectly overlaps early and late Bronze Age Armenia. So was there *any* population change there? Chalcolithic Aremnia is contemporaneous with Yamnaya btw.

- There doesn't seem to be any immediate problems, from PCA and ADMIXTURE, with modeling Yamnaya as Iranian_Neolithic + EHG (and also CHG the same way). Is this truly the case, or is there detail in the paper that contradicts this (and actually makes a case for Yamnaya as CHG+EHG)?

Essentially the question here is "Is there an excess of sharing by Yamnaya with CHG over and above what would be expected for an EHG+Iranian Neolithic composite? Or even is the opposite?".

(Now I do fully expect that Georgians *will* have an excess of sharing with CHG over and above what would be expected for a CHG proxy of Iranian Neolithic plus EHG.)

Nirjhar007 said...

Iran had EHG type ancestry from Mesolithic!. I guess this explains the small amount of Such ancestry present in S Asia .

Gioiello said...

Krefter's bullshit!

He said above that European mt not belonging to hg. U are at 99% of Middle Eastern Origin. First of all he could say what is Middle East, seen that also for the Y Israael/Jordan are very different from Iran and more from Northern Turkey practically similar to European hunter-gatherers. The "Natufian" mt have some subclades known also in Europe from so long (let's wait that Italian mt is tested as Italian Y, and Balkan one etc.) For instance there is a sample of K1a4b, with descendants in Middle east to day, but K1a4 is very likely older in Italy, and the same from other haplogroups, who may come from the Caucasus better than from "Middle East". Also about the origin of R0a2 and its ancientness in Italy I have written a lot, and so on.

Sam Hilsen said...

Does this make we EM123/136 Jews autochtonous? ;)

Gioiello said...

@ Sam

Of course it is very likely that those haplogroups present in many Jewish lineages all over the world have more probability to be Old Jews rather than those haplotypes with a MRCA after the diaspora, that my opponents say due to a bottleneck and I say due to introgression. Very likely hg. E is the oldest in Middle East and perhaps in oldest times the unique. Of course J arrived not more than 5000 years ago, and also these hgs may be old in Jews as also many R1b, but so far from the R-M343 tree of Sergey Malyshev only a few subclades seem old in Jews. We'll see from the next tests and above all from aDNA.

Matt said...

So more reading:

- The very high Basal Eurasian estimate in Mesolithic Iran suggests that Iranian Neolithic and Levant Neolithic may already have begun to mix with one another and the European / Siberian HGs?

- Natufians are probably going to be a very structured (North) African population, aren't they? Basically. One that no longer exists. As "no affinity of Natufians to sub-Saharan Africans is evident in our genome-wide analysis, as present-day sub-Saharan Africans do not share more alleles with Natufians than with other ancient Eurasians".

Yet Basal Eurasian is clearly quite ancient in the ME, and seems present before an Natufian incursion - "The idea of Natufians as a vector for the movement of Basal Eurasian ancestry into the Near East is also not supported by our data, as the Basal Eurasian ancestry in the Natufians (44±8%) is consistent with stemming from the same population as that in the Neolithic and Mesolithic populations of Iran, and is not greater than in those populations"

(which is a strike against the idea that Natufians themselves brought a set of farming pre-adapted genes into the ME, which spread with BE).

- Regional differentiation in the ancient Middle East seems more intense than between European and Siberian HGs. Particularly relative to the extremity of low population size.

So, all the findings where unsupervised ADMIXTURE kept digging out a West Asian, Levant-Mediterranean and "European" cluster (and then splitting the Levant-Mediterranean into West Med and SW Asian), rather than WHG, ANE and ENF were perhaps closer in a sense closer to the truth we find now than our supervised models after Laz 2013, where we were trying to force a model of WHG, ANE and ENF.

- The estimates of steppe ancestry in South Asians seem extreme, however, if you work from the assumption that Iranian Neolithic is more "extreme" than CHG and CHG is already admixed with EHG, that may help them make more sense. I'll be interested to see Davidski's modeling on this.

It does suggest that it's less likely that many present day "Northern European" traits (tall height, unusual pigmentation) actually spread with steppe ancestry though, if true. Or were *strongly* selected against.

- "We also document a cline of ANE ancestry across the east-west extent of Eurasia. Eastern Hunter Gatherers (EHG) derive ~3/4 of their ancestry from the ANE (Supplementary Information, section 11); Scandinavian hunter-gatherers7,8,13 319 (SHG) are a mix of EHG and WHG; and WHG are a mix of EHG and the Upper Paleolithic Bichon from Switzerland (Supplementary Information, section 7). Northwest Anatolians—with ancestry from a population related to European hunter-gatherers (Supplementary Information, section 7)—are better modelled if this ancestry is taken as more extreme than Bichon (Supplementary Information, section 10). "

No comment necessary. :)

... Well, actually comment is necessary, isn't it? They need to validate this against the findings in Fu et al 2016, on Ice Age Europe, which they've controlled for to some degree (e.g. using Ust Ishim as a validator for BE as they should, and not using ENA) but not really included in a robust sense. Fu et al has much broader scale groupings from the Villabruna cluster and evidence for admixture in some Villabruna by El Miron cluster (the Magdalenians).

Shaikorth said...

"Natufians are probably going to be a very structured (North) African population, aren't they?"

Quite possibly. Also even though direct Chimp SSA X Y doesn't seem to detect it here (ascertainment?), fst-ratios I posted earlier imply some connection to SSA, even relative to modern Near Easterners and ancient populations that supposedly have as much or more basal than Natufians.

Matt said...

@ Shaikorth, I was actually trying to write "Basal Eurasians are probably going to be a very structured (North) African population, aren't they?" but failed miserably, though thanks for the comment.

Other comments:

-Also, f3 admixture stats that make you go hmm....
BedouinB Iran_HotuIIIb Natufian 0.01384 4.1 32266
no evidence for Iranian_Neolithic related ancestry mixing with Natufian related ancestry in BedouinB.

This was their lowest score, and still positive.
(however the SNPs do kind of suck).

- Re: proportions in ED Fig 4, Makrani as the most Neolithic Iran South Asian population seems like it might be affected by African admixture in this population?

Likewise Cochin Jews, who obviously have quite a big wedge of Neolithic Levant ancestry that's contributing to their Neolithic Iran estimate.

Agree with upthread comments that they really should be modeling with later Iranian population and Chalcolithic Armenia as well, as much as still not 100% about qpAdm as a method. It would've been nice to have an ADMIXTURE based method (and perhaps f4 ratio as well) comparison as a "sanity check" here, as in the Cassidy et al (Bronze Age Rathlin paper).

(And generally, why no ADMIXTURE of the modern world dataset plus ancients?).

- Their qpGraph methods will benefit from being re-tested with all the Fu et al samples, not just Kostenki14 to check for consistency, since there's a cross historical timeslice there.

However, looks like they have one model Figure S4.11 that models Iran_Neolithic as EHG+Basal Euraian (38:62 ratio and plus lot of separating drift in Iran_Neolithic).

Kurti said...

"This led us to try one last model in which we model Steppe_EMBA as a 3-way mix of EHG, CHG, and Iran_ChL. The P-value for rank=2 is 0.241, so 3 streams of ancestry are consistent with the quadruple (Steppe_EMBA, EHG, CHG, Ira
n_ChL) and the fitted mixture proportions are 52.7% EHG, 18.1% CHG, 29.2% Iran_Ch "
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.

Kurti said...

My gues for Iran_N is R1 not R2. ;)

Kurti said...

Am I missing something? Or did the outcome of the paper shocked you guys so much that you are in denial now? How "Bury" the Out of Iran theory "completely" now if the paper obviously points out that there was geneflow from Iranian Plateau into the Steppes and than we have a P1 sample that could be anything from R1(R1a,R1b), R2 to Q.

My theory is still that Indo European likely evolved in the Steppes but is a creol language that appeared out of a fusion from Iranian Plateau herders and EHGs.

Kurti said...

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.

Kurti said...

I am still waiting for the samples from Eastern Iranian Platea and Central Asia, because my instinct tells me these will be slightly different in having more ANE.

Sam Hilsen said...

The only thing that really matters is that EM123 is autochtonous to Israel. Indo-Europeanness is irrelevant ;)

Azarov Dmitry said...

I guess now we can say for sure that both R1a and R1b came in Europe from the Iranian Plateau.

Gioiello said...

@ Sam
You know me very well, and you could spoke to me and not to an anonymous, but remember what I said: that Jews aren't sure to descend from Old Jews neither when they are hg. E or J. All your Stanford's PhD-s have been definitely defeated by me.

@ Azarov Dmitry
Where have you seen in these data that R1b and R1a came to Europe from the Iranian plateau? That P* haplotype doesn't demonstrate anything and at least it is R2 as Davidski said too. I remember you that R1b1a has been found in Villabruna, Italy, 14000 years ago and many R-L23 subclades in Samara, Russia.

Kurti said...

MA1 (Mal'ta) is modeled as ~28% Iranian Neolithic and 35% WHG like.

Either it is Mesolithic Iranian admixture in Mal'ta or Mal'ta admixture in Neolithic Iran. So much to there is no ANE in Neolithic Iran.

I think the reason for this conclusion is, that they believe Mal'ta is Iranian Plateau admixed.

Kurti said...

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

EHG on itself is modeled as 75-80% WHG, ~7% Iranian Neolithic, ~10% CHG and some ~3% dark blue I can't tell what it is.

andrew said...

Huge! The most surprising in the Y-DNA department is:

I0867: H2 (PPNB). Very surprising to find what is today a private South Asian haplogroup in the early Neolithic, without appearances anywhere inbetween.

Andres Folg said...

Results mostly as expected. I guess I1945 is R1b.

Andres Folg said...

H2 a South Asian haplogroup? you are highly lost!

Kurti said...

Gioello said

"P* haplotype doesn't demonstrate anything and at least it is R2 as Davidski said too"

Are you seriously selling us Davids speculation as a prove? What and how did he demonstrate that it is R2? He said "I ASSUME it is R2".

There is absolutely no reason to ASSUME it is rather R2 than R1.

I ASSUME it is rather R1 than R2. However where you find R2, R1 shouldn't be far away anyways.

As I said in the past R1 is such a old Haplogroup by Neolithic at least it should have been widespred around whole Eurasia. So conclusions like "all R1 came from place x to place y" are just nonsense.

Andres Folg said...

I will bet that I1945 is a Gioiello and Villalbruna cousin :) Gioiello should start to seek for another refugium.

Coldmountains said...

@andrew @andres

Not surprising at all. H was found in Neolithic Anatolia and if i remember it correctly also among European Neolithic Farmers which both lacked any South Asian admixture. H has probably a very complicated history could be Basal Eurasian or like IJ some Hunter Gather lineage which spread over vast tegion and was absorbed byfarmers

Arch Hades said...

Two things.
1. proves haplogroup J2 comes from the Caucasus, not the Levant. All Levantine farmers lack J2.
2. "Steppe ancestry" will get bloated in Iran and South Asia unless we can get an idea of how much CHG like ancestry in South Asia and Iran is from the steppe and not earlier migrations. The Neolithic Iranians are very much like CHGs.

Davidski said...

@Kurti

Check out the Y-DNA list I posted above.

Loads of R1, R1a and R1b in the ancient Near East, eh?

Haha.

Davidski said...

@Azarov Dmitry

We can now say for sure that both R1a and R1b did not come to Europe from the Iranian Plateau.

Jingus Jendal said...

@Nirjhar

It must really, really suck to be an OIT supporter right about now.
Whenever Harrapan Y-DNA is finally released, and there's no R1a, are you going to actually make good on your promise(made last year on this blog) to go away? Or are you just going to keep making dumb rationalizations?

Kurti said...

The moment the antis have no more arguments left, they make just some very weird statements.

Dave Who said ancient the Near East was full of R?? Do you actually read comments? I always said we will find R Haplogroups on the Iranian Plateau, as well South_Central Asia, prior to Bronze Age. I was confirmed. Thats it no more need for talk

Have a nice day ;)

Dude ManBro said...

The comment section for this blog is a magnet for nut bars. Funny how commenters here believe this pre-print supports their stance on the IE issue, regardless of whether they support the Kurgan theory, a Near Eastern origin, Central Asian origin or the zombie OIT.

Stay classy, guys. Stay classy.

Davidski said...

@Jingus Jendal

Nirjhar prefers Out of Iran for Proto-Indo-Europeans and Out of South Central Asia for Proto-Indo-Iranians.

But neither looks plausible, especially after this latest round of results.

R1a-M417 and R1b-M269 obviously expanded from the Eurasian steppes during the Bronze Age. And that essentially solves the Indo-European question.

Rob said...

@ Kurti


"My theory is still that Indo European likely evolved in the Steppes but is a creol language that appeared out of a fusion from Iranian Plateau herders and EHGs."

Bro- PIE isn't a creole. There are technical reasons which I won't go into, but it's not really too debatable . IE is a 'normal' language

About the P* in Iran.
Yes itll be interesting to see what it is.

AWood said...

The Y data defined as CT is frustrating but it appears that G and H2 (old F) were the predominant groups of EEF and the eastern Iran types were J1/J2 who pushed westwards and/or were jockeying for territory. E1b were hunter gatherers of the Levant who appear to have adopted farming from the G/H2 guys who were based out of western Anatolia. Depending on what exactly CT is, L and T fit in there somehow as well...of course small numbers of hunter gatherers R and I were probably in southern Europe and may turn up during the Neolithic Near Eastern period as well. I suspect most of the R found in the Near East is of Late Bronze Age or Iron Age period.

Iranocentrist said...

Yes it is quite obviouse now that Iran was the source of steppe IE's.

Sam Hilsen said...

E1b adopted farming from Anatolians? Idk about all that but the Natufians developed quite a few things independently of their northern neighbours, and were settled before agriculture even developed in their area.

Davidski said...

@Iranocentrist

Yes it is quite obvious now that Iran was the source of steppe IE's.

Eastern European Hunter-Gatherers became steppe IEs, so nope, sorry.

You're turning into a caricature of yourself. The Iranian version of Nirjhar.

Dude ManBro said...

If the Iranian samples had come back with substantial amounts of Y-DNA R1, then maybe the idea of an Iranian PIE homeland would be more likely.

I do not think it probable that a people who spoke a language (PIE) with words for bride price, son's wife and brother's wife but not words for daughter's husband or sister's husband spread said language via female exogamy.

Not impossible, but if someone put a gun to my head and told me to choose the PIE Urheimat, it still wouldn't be the Iranian plateau.

Arch Hades said...

So I have some questions now about Neolithic Iran. Since they're related to CHGs can we say that they are the product of CHGs migrating South, since we know CHGs are native to Upper Paleolithic Georgia since at least 11,000 BC. Or is it that you guys think they were always in Iran? Could they have been present in Northern Iran for as long as their relatives were in Georgia?

andrew said...

"Yes it is quite obvious now that Iran was the source of steppe IE's.

Eastern European Hunter-Gatherers became steppe IEs, so nope, sorry."

At page 8, lines 265-267: "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 short answer is that EHG and Iranians contributed roughly equally to the Bronze Age steppe population which either included or was immediately descendant from the Proto-Indo-Europeans. So, you're both wrong.

Davidski said...

@Arch

It looks like CHG-related populations lived in Iran as far back as the Ice Age. They weren't CHG proper, but closely related.

However, it seems that there was a rush of this type of admixture from somewhere in the north, probably CHG proper from the Caucasus, into Iran during the Chalcolithic.

This matches archaeological data as far as I know.

It's possible that the same groups that moved into Iran made some sort of impact on the steppe as well, especially if they were expanding from the Caucasus. But if they did, it was via female exogamy with steppe people.

In other words, steppe males took southern brides.

Davidski said...

@andrew

Read the supp info more closely. Page 83.

Nonetheless the 3-way model is also plausible as it suggests an explanation for the shared genetic drift between Steppe_EMBA and the Anatolian and Levantine Neolithic (underestimated when CHG alone is the southern population; Table S7.12), and makes geographical sense as admixture from the Near East could have arrived on the steppe via the Caucasian isthmus where an addition of CHG ancestry could have occurred.

In other words, you shouldn't take the main models too literally, even if they're statistically most parsimonious.

There's actually no direct evidence in this paper that anyone from Iran ever made it onto the steppe during the Chalcolithic or Bronze Age. Not an iota.

And I'll also add that in my opinion Steppe_EMBA is really a mixture of EHG, CHG and Chalcolithic Balkans.

Rob said...

So whilst Central Europe - steppe homogenised by the EBA, so too did the near east- Central Asia region (albeit less so due to higher densities and greater stratification).

Azarov Dmitry said...

@Davidski
"We can now say for sure that both R1a and R1b did not come to Europe from the Iranian Plateau."


If you take into consideration all the available data (genetic + linguistic + archeology) you’ll see that the Iranian Plateau is the only possible option.

Davidski said...

@ Azarov Dmitry

If you take into consideration all the available data (genetic + linguistic + archeology) you’ll see that the Iranian Plateau is the only possible option.

Eastern European Hunter-Gatherers and R1-rich Kurgan people didn't come from the Iranian Plateau. So you're wrong.

Apóstolos Papaðimitríu said...

'R1a-M417 and R1b-M269 obviously expanded from the Eurasian steppes during the Bronze Age. And that essentially solves the Indo-European question.'

What if they spread from there but were not Indo-Europeans? Scythians even had a kumis-like dairy product. The word 'Kipchak' means blonde Saka. 'Yakuts' identify as Saka. Greeks called Pechenegs and other Turkic and Hunic groups 'Scythians'. In an Armenian chronicle Pechenegs are descibed as an 'all archer army'.

Kurti said...

[QUOTE] An interesting aspect of this model is that it derives both Natufians and Iran_N from Basal Eurasians but Natufians have ancestry from a
population related to WHG, while Iran_N has ancestry related to EHG. Natufians and Iran_N may themselves reside on clines of WHG-related/EHG-related admixture. The fact that these two populations are differentially related to European hunter-gatherers can be directly seen from the following statistics:



MA1, EHG, SHG, Switzerland_HG are consistent with having no Basal Eurasian ancestry, while at least some such ancestry is inferred for the remaining populations.Neolithic Iran and Natufians could be derived from the same Basal Eurasian population but are genetically closer to EHG and WHG respectively We take the model of Fig. S4.9 and attempt to fit Natufians as a mixture of the same Basal Eurasian population that contributes to Iran_N and any other population of the tree. Several solutions are feasible, and we show the best one (lowest ADMIXTUREGRAPH score) in Fig. S4.10.
We can add both EHG and MA1 as simple branches to the model structure of Fig. S4.10 and show the results in Fig. S4.11. An interesting aspect of this model is that it derives both Natufians and Iran_N from Basal Eurasians but Natufians have ancestry from a population related to WHG, while Iran_N has ancestry related to EHG. Natufians and Iran_N may themselves reside on clines of WHG-related/EHG-related admixture. The fact that these two
populations are differentially related to European hunter-gatherers can be directly seen from the following statistics: suggests
that the singleton individual from Hotu (Iran_HotuIIIb) was shifted towards EHG along the Iran_N/EHG cline, albeit it does not reach |Z|>3. There is uncertainty about the date of Iran_HotuIIIb, as it is not certain that it is of Mesolithic age and thus predates the Neolithic of Iran from Ganj Dareh.
The fact that the Caucasus hunter-gatherers (CHG) (who are definitely pre-Neolithic) have extra EHG-related ancestry is also supportive of a substantial antiquity of this element in the Caucasus-Iran region. It is not clear whether the hunter-gatherers preceding the Neolithic in Ganj Dareh were similar to Iran_HotuIIIb or the CHG and their EHG affinity was diluted during Neolithization, or whether they are descended from an unsampled hunter-gatherer population that already had this reduced affinity to the EHG....


Thus it is rather the Mesolithic of Iran that shares more alleles with these eastern European groups than the Neolithic. Tentatively, this might suggest that the pre-Neolithic population of Iran had an affinity to the EHG/Ancient North Eurasians that was diluted during the Neolithic, although the lack of negative f4-statistics does not allow us to discern what is the source of this dilution. Alternatively, there was no dilution, but the Neolithic of Iran was descended
from an unsampled Mesolithic population.[/QUOTE]

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.

Lathdrinor said...

"There are numerous cases where the language of the females becomes dominant eventually. English is the best example against both the Scandinavian males and French speaking Normans."

Language change doesn't necessarily involve any significant change in DNA, and are more the result of socio-political changes, but just for the sake of argument, trying to paint Anglo-Saxon linguistic survival as female linguistic dominance is hilarious, as most female lineages in Britain are liable to have been pre-Anglo-Saxon.

In fact, Scandinavians [Vikings] and the Normans had very limited genetic impact on the population of England whilst the Anglo-Saxons, the actual forebears of the English language, had a significant impact, estimated at 30% by Leslie et. al (2015). English is a Germanic language, and the Y-DNA of Englishmen contain a significant percentage of R1b-S21/U106, which has been called "Germanic" by not a few scholars. Thus, even were to examine the English case, the theory falls apart.

This also applies to the rest of the people trying to associate early Neolithic population movements with linguistic lineages. Even proto-Indo-European isn't that ancient, and the same is probably true of proto-Afro-Asiatic. The paper is of no great surprise to me, but then I've always assumed that R1a/R1b did not come from the Near East. It's nice to see a bit of evidence. And I fail to see how it changes the popular view of proto-Indo-European history, though I might be behind on that.

andrew said...

@Davidski

"There's actually no direct evidence in this paper that anyone from Iran ever made it onto the steppe during the Chalcolithic or Bronze Age. Not an iota.

And I'll also add that in my opinion Steppe_EMBA is really a mixture of EHG, CHG and Chalcolithic Balkans."

The fact that you prefer a less parsimonious explanation than the one given in the paper as its primary hypothesis does not justify dismissing the paper's primary hypothesis out of hand with a "nope". Also, it is a straw man to say that no individual from Iran ever made it onto the steppe during the Chalcolithic or Bronze Age, although I'm sure that at least a few did.

The hypothesis supported by the genetic data instead is that 43% of steppe is derived from the Iranian Chalcolithic. It is entirely possible that this could have occurred over several generations of intermediate migration via either the Caucasus or Central Asia.

In particular, the hypothesis the Chalcolithic or Bronze Age Caucasians contributed to the Steppe population has ample archaeological and historical linguistic support, and the hypothesis that Iranian Chalcolithic populations were an important source population for Chalcolithic Caucasians likewise has archaeological and historical linguistic support.

Indeed, the genetic evidence in this paper tends to show, roughly speaking a three gene pools of early farmers - Levantine, Anatolian and Iranian (to oversimplify) and there is ever reason to think that the famers and pioneering metallurgists of the Caucasus had little demic contribution from the Levatine cluster and a lot of contribution from the Iranian cluster.

The archaeological evidence also makes no very persuasive argument for preferring a Balkan source (where metallurgy developed a bit later and where Kurgans type burial practices were a fairly late development) to a Caucasian demic contribution (where metallurgy developed a bit earlier and where there is continuity of Kurgan-like burial practices) to the Steppe people in the Chalcolithic and indeed the genetics seem to favor a Caucasian source which would be more Iranian-like to a Balkan one which would be more EEF/Anatolian-like as a demic contribution.

While I recognize that you are thinking of CHG in terms of a genetic component, rather than a true archaeologial culture, it is also pretty clear archaeologically, the Steppe people received much of their technological package from a farming and metal using culture and not from actual hunter-gathers. Indeed, I'm not aware of any evidence to support the idea that there were still any hunter-gatherers in the Caucasus by the Chalcolithic, even if the local farmers may have had significant genetic continuity with the hunter-gatherers that preceded them in the area.

Colin Welling said...

@davidski "From Eastern Europe."

Yup.

Even though it was already obvious, this paper has shown that the Steppe peoples migrated from Eastern Europe into all of the IE speaking areas (Europe, Middle East, and South Asia). Clearly these steppe people are the last link we have between all IE people. They must be the PIE people.

To those that still want to find wiggle room, you can't. The PIE problem is effectively solved. The last link between IE peoples are these Steppe folk. By definition that is PIE...

For anyone who wants to talk about Pre PIE... If it is a thing, I would side with david in thinking that it wasn't Caucasus/Iranian women who brought their language to the steppe and then the steppe people moved into the middle east and erased all evidence of this pre PIE language. You would think that if pre PIE was actually carried by iranian women, some remnants of pre PIE would have survived in Iran and India. If pre PIE did exist, it likely succumbed to a local development of PIE.

andrew said...

@Rob @Kurti

""My theory is still that Indo European likely evolved in the Steppes but is a creol language that appeared out of a fusion from Iranian Plateau herders and EHGs."

Bro- PIE isn't a creole. There are technical reasons which I won't go into, but it's not really too debatable . IE is a 'normal' language "

All languages come from somewhere, and not necessarily in a pure tree-like evolutionary form. Kurti's articulation of Indo-European as a technical "creole" may not be true in the narrow sense, but it is sensible to believe that Indo-European ethnogenesis took place on the steppe and that the language spoken by the newly arising culture is not a straightforward direct daughter language of either the LBK farmers or of the hunter-gatherers who inhabited the steppe before them, and there is archaeological evidence of communities on the steppe at the estimated time of Indo-European ethnogenesis that had ethnically mixed populations that drew on both farmer and steppe hunter-gatherer populations. So, it isn't unreasonable to think that more than one language family made meaningful lexical, phonetic and grammatical contributions to Proto-Indo-European.

Perhaps a better technical description of the formation of Indo-European may have been that there was a superstrate parent language and a substrate language whose relative status levels where so nearly equal that it was hard to tell which was which from subsequent linguistic data resulting in a maximal substrate linguistic influence.

The process might be compared to a more extreme version of the process by which the Japanese language family came to be with a primary source that was probably a language of an ancient, probably now extinct Korean language family, but with such heavy lexical and written language contributions from Chinese that Chinese is, if not is mother, at least its step-father.

As some other examples, Dravidian languages had not just lexical but strong grammatical and phonetic influences on Hindi as a substrate language, and the Semitic Akkadian language had strong grammatical and phonetic influences on Sumerian before it superseded the Sumerian language entirely.

Lathdrinor said...

"Even though it was already obvious, this paper has shown that the Steppe peoples migrated from Eastern Europe into all of the IE speaking areas (Europe, Middle East, and South Asia)."

This paper presents no new samples from Europe, so insofar as that question is answered, it isn't from this paper, but from earlier ones. Still I do have to agree, given that we now have samples from both Ice Age Europe and the Neolithic Near East to support the scarcity of R1a/R1b outside of Eastern Europe. But it could also be that R1a/R1b were simply rare before a certain explosive expansion period, and were confined to regions that have not yet been sampled; we'll need early Neolithic samples from Eastern Europe to corroborate the idea that it was the R1a/R1b homeland, so the verdict is still out.

Colin Welling said...

"Iranocentrist said...
Yes it is quite obviouse now that Iran was the source of steppe IE's."

Do you realize that you are basically only arguing where Pre PIE came from. The last shared heritage of all IE peoples is the steppe. The most recent common ancestor is what makes something "proto". Iranian and Indic came from the steppe. You can try to argue that pre PIE came from Iran... but Iranian came from the steppe.

Rob said...

@ Andrew


Yes I agree. I was merely commenting from a narrowy technical sense

@ Colin.

We still need data from Bronze Age Anatolia & Greece to document steppe admixutre.

Colin Welling said...

@lathdrinor "This paper presents no new samples from Europe, so insofar as that question is answered, it isn't from this paper, but from earlier ones."

True, but we now know Iran didn't harbor any EHG or steppe like signature prior to the bronze age. We can extrapolate that there was not EHG gradient that went south of steppe prior to the enolithic. Therefore, the steppe like signature in indians came from the steppe.

postneo said...

@Rob, Kurti

On PIE being normal and not a creole. I am neutral on the subject but all languages are pidgins then creoles to some extent especially at the beginning. and I don't understand such a rigid classification. English and other languages IE seem to have creole elements.

Similarly DNA and social groupings would work in a similar fashion. Zorastrian/parsi DNA is modern but somewhat eye opening and something I never looked at before. I assumed they would have higher R1a than fellow Iranians, but they don't.

Its a snapshot of an old IE speaking community. they would have a growth phase attracting new converts and DNA, a stable endogamy phase and then decay after islam. What it tells us is that not all IE speakers had R1 ydna. While this may seem unremarkable, we see too much of these blanket assumptions nowadays.

As for R lineages in western Iran I think they will be found in similar proportion to what is found there today, Lets see.

Rob said...

@ PostNeo

"On PIE being normal and not a creole. I am neutral on the subject but all languages are pidgins then creoles to some extent especially at the beginning. and I don't understand such a rigid classification. English and other languages IE seem to have creole elements. "

Well, these 'rigid' classifications exist to clarify the social aspect of language inheritance. Its does make a difference, if details matter to you.

Creoles are unusual events, they happen in modern Colonial period when a whole bunch of people are forcibly lumped together. As Andrew stated, this is different to language shifting and inherited substratum effects.

Colin Welling said...

@ rob

the greeks don't really matter. Italo-celtic, iranian, and Indic are only connect by PIE. There last genetic connection, the steppe, is strong and has the timing of PIE. Therefore the steppe needs to be PIE. If greek lacked steppe, then I would just say that the greeks were language converts.

You can still make the argument that anatolian was the original early PIE, then its daughter, late PIE, moved into the steppe explaining the steppe connection between enland and india but the anatolian hypothesis is already debunked imo.

Rob said...

Yeah the steppe might be the last common thread, but saying two of the major & earliest languages (Greek & Anatolian) don;t matter just sounds a bit silly to me.

What is a "language convert ' ? Is it something like western champagne liberals suddenly becoming Buddhist & vegan ?

Lathdrinor said...

"What is a "language convert ' ? Is it something like western champagne liberals suddenly becoming Buddhist & vegan ?"

I imagine it's similar to being a religious convert - more culture, less genetics. And there certainly are examples of language converts. India and English being an example, as despite the Indo-European link, we can safely say that India was not English speaking prior to the British Empire, and that the situation today was not the result of significant English genetic impact on Indians.

Davidski said...

@andrew

The hypothesis supported by the genetic data instead is that 43% of steppe is derived from the Iranian Chalcolithic.

Nope, the hypothesis supported by the genetic data is that ~43% of Steppe_EMBA ancestry is related to Iranian Chalcolithic.

Big difference, and a problem, because Iranian Chalcolithic is different from Iranian Neolithic.

@Lathdrinor

But it could also be that R1a/R1b were simply rare before a certain explosive expansion period, and were confined to regions that have not yet been sampled; we'll need early Neolithic samples from Eastern Europe to corroborate the idea that it was the R1a/R1b homeland, so the verdict is still out.

And who were the Khvalynsk men? Migrants from Iran? Because to me they look a hell of a lot like native Eastern Europeans.

http://eurogenes.blogspot.com.au/2015/11/the-khvalynsk-men.html

Rob said...

Yes we can all imagine what a language convert might entail, but my sarcasm was merely pointing out the absurdity of such an idea.

Wishy-washy colonialist analogies do not suffice for a vastly different period, in a different place. Industrialist England and their colonization of the subcontinent is irrelavant for the Copper Age interactions across Europe, the steppe & near East. Same deal with all the misguided use of America & the fate of its natives

Bronze Age Anatolia was teeming with IE speakers. The Myceneans were obviously also IE. Now, given that these regions were densely populated, and had developed heirarchical systems already by late M4, why should they 'convert' all of a sudden to the language of some fledgeling cattle-herders from the steppes ?

The only way this "conversion" is possible, is by outright colonization- at some point between 4000 BC and 200o BC. Which is to say, not a 'conversion' event at all.

So we should expect to see steppe admixture in EBA- MBA Greece & Anatolia

Davidski said...

Of course Bronze Age Greeks and Anatolians will show steppe admixture.

Just take a look how the Y-chromosome landscape of the Near East changed from the Neolithic to the present.

Y-HG R1 made a fairly big impact, and in many instances it had to have come directly with steppe peoples.

Rob said...

It's a done deal, them ;)

Lathdrinor said...

"And who were the Khvalynsk men? Migrants from Iran? Because to me they look a hell of a lot like native Eastern Europeans.

http://eurogenes.blogspot.com.au/2015/11/the-khvalynsk-men.html"

They do, but where did they come from, and were they the only R during the period? After all, we have an Epigravettian R1b from Italy to consider, from Paleolithic contexts. If R1b could spread all the way to Italy during the Paleolithic, it could've spread to other regions before the Bronze period, in which case the question is: where and from where? It is not yet time to say that Samara/Khvalynsk was the *only* center of R1 during the Neolithic. Those cultures may have played a huge role in the distribution of R1 today, but they may not have been the earliest homeland of R1 and they may not have been the only regions from which R1 spread. To me the Khvalynsk sample serves more as a repeat of the Yamnaya evidence, indicating that the Volga region was in fact an early center of R1, but not necessarily the only one.

Though it might have been the only one that mattered. We'll see.

Grey said...

We've come along way from Basal farmers from the Levant spreading everywhere over local HGs.

I think we're partly looking at a recurring pattern of early farmers creating their own nemesis i.e. they expand to the border of farming viability and beyond that border they catalyse HGs into pastoralists and eventually the pastoralists beyond the border get strong enough to come over the border and destroy /displace the farmers.

#

"a population related to people of the Iran Chalcolithic contributed ~43% of the
267 ancestry of early Bronze Age populations of the steppe"

related to, not same as

somewhere in between which expanded both ways might be Caspian coast?

#

a population with a military edge can defeat a larger population - so hypothetical

pop A 100 m/f
pop B 500 m/f
pop A defeats pop B
future reproduction based on 100 pop A males and 100 A + 500 B females
= 100% A ydna, 1/6 A mtdna 5/6 B mtdna, 60% A adna 40% B adna

hypothetically

#

increasingly feeling (to me) that LGM refuges were water based (cos fish cold-blooded i guess) including maybe
- franco cantabria
- adriatic
- aegean
- black / caspian seas
- persian gulf
- nile delta

in particular wondering now (unless i've misunderstood something) if Basal came from the flooded persian gulf?

#

"Regional differentiation in the ancient Middle East seems more intense than between European and Siberian HGs. Particularly relative to the extremity of low population size."

Mountains i guess.

Grey said...

"60% A adna 40% B adna"

ish

la señora bibiloni said...

Fascinating paper and fascinating thread. I love to read this blog because of the papers it features and the bloggers' comments, even if any R1b that pops up in a non-Steppe region will always be identified as a stubborn Steppe guy who got lost, refused to ask for directions and ended up far from home

Davidski said...

It sounds like the genotype data might be available as early as next week, just prior to publication.

bellbeakerblogger said...

Maybe I'm misreading, but they don't appear to exclude M73 from the boy I1945 (GD16), seems strange not to address for this area.

Krefter said...

@Everyone,

Quote from Davidski.
"Just take a look how the Y-chromosome landscape of the Near East changed from the Neolithic to the present.

Y-HG R1 made a fairly big impact"

You got to hammer this into your minds. Western Asia isn't the home of R1 we, included myself, thought it was. It's at the receiving end just as Europe is.

Most R1 in the Western Asia is either R1a-Z93 or R1b-Z2103, both of whom have been found on the Steppe. The Basal R1s do exist in Western Asia but are a small minority. R1b-V88 in the Levant is another story.

The mystery of the origin of 90% of modern R1 is solved. It's from young(less than 8,000 years old) founder effects that occurred around Russia and Ukraine and then expanded in the last 5,000 years.

Davidski said...

The likes of Kurti and Nirjhar will be in denial of this for another decade or so.

Gioiello said...

@ Lathrinor

I could interpret your nickname as "Latrus", Latrus idearum mearum. This is my theory of an "Italian Refugium from at least 10 years. Anyway I thank you, because you are becoming in understanding the truth that pretty all the others, above all the PhD of Stanford and elsewhere, are trying to hide.

Lathdrinor has left a new comment on the post "The genetic structure of the world's first farmers...":
"And who were the Khvalynsk men? Migrants from Iran? Because to me they look a hell of a lot like native Eastern Europeans.

http://eurogenes.blogspot.com.au/2015/11/the-khvalynsk-men.html"

They do, but where did they come from, and were they the only R during the period? After all, we have an Epigravettian R1b from Italy to consider, from Paleolithic contexts. If R1b could spread all the way to Italy during the Paleolithic, it could've spread to other regions before the Bronze period, in which case the question is: where and from where? It is not yet time to say that Samara/Khvalynsk was the *only* center of R1 during the Neolithic. Those cultures may have played a huge role in the distribution of R1 today, but they may not have been the earliest homeland of R1 and they may not have been the only regions from which R1 spread. To me the Khvalynsk sample serves more as a repeat of the Yamnaya evidence, indicating that the Volga region was in fact an early center of R1, but not necessarily the only one.
Though it might have been the only one that mattered. We'll see.

Andres Folg said...

As fas as I can see is that 1 out of 1 Neolithic Iranian sample is P (likely R1b) so, how can someone claim that R1b don't came from the Iranian Plateau? What we will see if we test 5 more ancient remains? Perhaps, other P (R1b) groups? Perhaps, the source of Western R1b.

Davidski said...

As fas as I can see is that 1 out of 1 Neolithic Iranian sample is P (likely R1b) so, how can someone claim that R1b don't came from the Iranian Plateau?

Why then is R1b so rare in South Asia, where Neolithic Iranian ancestry peaks today?

Wouldn't it make more sense if that sample was R2?

Andres Folg said...

Also interesting to see that I1707 is negative for T1a1 when I0795 from the ancient Europe is positive for T1a1. This mean that the Levant isn't the source for T1a1 in the ancient Europe, they both share common ancestor as far as 20000ybp.

Colin Welling said...

@rob

Wishy-washy colonialist analogies do not suffice for a vastly different period

You are missing the point. It is easier to explain the greeks as having learned a language from steppe people rather than any other alternative. Thats all I'm saying. You should know the Greek is actually a language that branched off after Italo celtic but not before Indo Iranian. If you think that PIE wasn't steppe then explain how steppe manage to get into Italo Celts and Indo Iranians but not the greeks? Again, the latest linguistic connection between English and Indian is PIE and the latest genetic connection is steppe.

I expect the Greeks to have steppe ancestry but nothing fundamental will change if they didn't.

Davidski said...

@Andres Folg

As fas as I can see is that 1 out of 1 Neolithic Iranian sample is P (likely R1b).

Here are all the samples from Iran, early Neolithic to Chalcolithic. First two are Neolithic.

I1945: P1(xQ, R1b1a2, R1a1a1b1a1b, R1a1a1b1a3a, R1a1a1b2a2a)
I1949: CT
I1671: G2a1(xG2a1a)
I1662: J(xJ1a, J2a1, J2b)
I1674: G1a(xG1a1)

Can't see any R1 here. The P1 doesn't qualify, because it might be R2 or some dead R line that no longer exists.

Colin Welling said...

@Geo "It is not yet time to say that Samara/Khvalynsk was the *only* center of R1 during the Neolithic. "

It is the center for m269, which has to do with the IE question. I have no idea how r1b came into western russia. I doubt it was via the middle east or we would have seen a lot more r1b in neolithic samples or a lot more in india.

Krefter said...

@Collin,

Greeks have Steppe ancestry. Current estimates have it varying from 20-30% in Greece. That's not small at all. Steppe ancestry has definitely been in Greece since the Bronze age. We already have unpublished confirmation it was in Croatia back then.

Gioiello said...

@ Colin Welling
"@Geo "It is not yet time to say that Samara/Khvalynsk was the *only* center of R1 during the Neolithic. "
It is the center for m269, which has to do with the IE question. I have no idea how r1b came into western russia. I doubt it was via the middle east or we would have seen a lot more r1b in neolithic samples or a lot more in india.

Colin, at Samara we have only some subclades of R-L23*. There lack the upstream and the downstream subclades, thus there wasn't the origin of R1b1-L389 and subclades. Above all there hasn't been found R-L51, the ancestor of all the downstream subclades of Western Europe.
As it has been found R1b1a* at Villabruna 14000 years ago, you will see, when these PhDs will decide to test other samples from Tyrrhenian Italy and other places of Western Europe where R1b migrated from the "Italian Refugium", where the R1b1a2-M269 was born. Your statement is based upon nothing.

Rob said...

@ Colin

No, you're missing the point bud. Im not saying that PIE didn't expand from the steppe, but you are inventing ideas about language switching without any explanatory details, as if by special pleading.
What's more, the details of your vision of the tree are simply false, as Greek split more or less equally with IA & celtic. In fact, Greek is probably a lot older than Celtic. To top it all off, you come up with pearlers like "the latest linguistic connection between English & Indian is IE".

Simon_W said...

The early speakers of the Anatolian branch, i.e. the Hittites, Luwians and Palaics, do matter a lot, because by all accounts the Anatolian branch is the most divergent of all IE branches. This may be reasonably explained by the assumption that they split off before all other IEs split. (Although there are other, less plausible theories, like that they were more strongly influenced by the non-IE substrate than all other branches.) For that reason the genetic affinities of the early IE Anatolians do matter even more than the origin of the Indo-Iranians. Because even if all other IEs were from the steppe, if the Anatolians were not, then PIE wasn't from the steppe.

Andres Folg said...

Davidski,

According to the authors "It was ancestral for downstream haplogroups Q (F1237.1, FGC4603), R1b1a2 (CTS12478), R1a1a1b1a1b (CTS11962), R1a1a1b1a3a (L448), and R1a1a1b2a2a (Z2123)"

They use "downstream" for "R1b1a2" IF P1 is upstream "R1b1a2", P1 is upstream R1b, then R1b is a possibility for this sample.

Are they wrong?

Gioiello said...

@ Simon_W
"For that reason the genetic affinities of the early IE Anatolians do matter even more than the origin of the Indo-Iranians. Because even if all other IEs were from the steppe, if the Anatolians were not, then PIE wasn't from the steppe".

Just because Hittite retains laryngeals, and the unique IE language which retains laryngeals for what I know is Albanian, I think that the origin of IE should be westernmost than it is usually thought: the Balkans, and before also westernermost...
Of course I think that from the steppes expanded the satem IE languages, but not the oldest centum ones.

Gioiello said...

@ Andres Folg
"They use "downstream" for "R1b1a2" IF P1 is upstream "R1b1a2", P1 is upstream R1b, then R1b is a possibility for this sample.

Are they wrong?"

Of course you are right, and only the Bam file will say which is its subclade. That it could be an Hg. Q or R2 is more likely, but of course we may not exclude some form of R1b or why not R1a. It is right to wait that Genetiker or some other reads the Bam file when it will be at our disposal. But if R1b were in Old Middle East we should have found some sample of it, but so far nothing of nothing from Natufians to even Western Anatolians who were very likeleìy linked to Western European hunter-gatherers. But let's wait...

Rob said...

@ Simon_W

Thanks. Eloquently put.

Colin Welling said...

@rob,

"but you are inventing ideas about language switching without any explanatory details"

If PIE was steppe, and greeks don't have steppe, then it was exclusively a language transfer. Thats just logic.

The point your are still missing, probably willfully, is that its much easier to explain away a hypothetical lack of steppe in ancient greeks with the kurgan hypothesis, than to explain steppe admixture in Italo Celts, Iranians, and Indians without the kurgan hypothesis. The Kurgan Hypothesis stands regardless of whether or not the early greeks had steppe in them.

"We still need data from Bronze Age Anatolia & Greece to document steppe admixture."

No we don't.

"In fact, Greek is probably a lot older than Celtic"

I said Italo Celtic. Its pretty sad when you lose sight of an argument, make it about technicalities, but still get that wrong. The branch that led to Italo celtic is the third branching in the Ringe et al phylogeny. The point is that the greeks did not break off before the Italo Celts and Iranians differentiated from one another, which would have allowed the possibility for the latter two to "enter" the steppes after the greeks had already taken off. Didn't happen.

Colin Welling said...

@simon,

"For that reason the genetic affinities of the early IE Anatolians do matter even more than the origin of the Indo-Iranians. Because even if all other IEs were from the steppe, if the Anatolians were not, then PIE wasn't from the steppe."

You are correct. Thats why I said the greeks don't matter. The anatolians, on the other hand do matter. If they didn't have steppe dna then that would pose some problems for the steppe hypothesis and leave open the possibility that the earliest PIE didn't start on the steppe. Still though, the anatolian hypothesis has too many holes imo.

Colin Welling said...

@Geo, What are you disagreeing with? L23 is the relevant r1b haplogroup for IE. It was obviously in the Yamnaya and the bell beakers who introduced steppe ancestry to western europe. Im sure L51 was also (western) steppe derived.

Are you questioning if L23 was born around the steppe?

Gioiello said...

@ Davidski
"I1945: P1(xQ, R1b1a2, R1a1a1b1a1b, R1a1a1b1a3a, R1a1a1b2a2a)
"

Having been found I1945 negative for one SNP at the Q* level (FGC4603) doesn't exclude all the Q* haplogroup, which has other 12 SNPs on the same level in the YFull tree.

Gioiello said...

@Colin Welling

"@Geo, What are you disagreeing with? L23 is the relevant r1b haplogroup for IE. It was obviously in the Yamnaya and the bell beakers who introduced steppe ancestry to western europe. Im sure L51 was also (western) steppe derived.

Are you questioning if L23 was born around the steppe?"

Have I to take "Geo" as my name? In what yousay there are many presuppositions not demonstrated:
1) that R-L23 is the relevant R1b haplogroup for IE
2) that Bell Beakers derive from Yamnaya
3) that R-L51 will be found in Western steppes, when I demonstrated that to-day the sister clade R1b-L51-PF7589 is pretty at o,oo% Easterward Italy.

Andres Folg said...

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 necessary discarded? NO!

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

Anyone knows when CTS12478 appeared? Beacause between 6400ybp and 10.000ybp there are 3600 years for accumulate new mutations! What if CTS12478 is younger than the sample?

Olympus Mons said...

As per my thesis...

river Volga while other turn all the way east moving around the east side of the Caspian sea and making a blob of R1b north of Iran and the other following the river or maybe a mix of the two just settle in the southern Caucasus to what is today South Georgia, Armenia and west Azerbaijan. Or maybe some actually came from much closer from the Dnieper basin and just crossed the mountains."


Since this is a speculative post... It looks like this P* was the part of the r1b moving east of the Caspian...going nothbound, crossing araxes river and settling in shulaveri shomu. Ok suits me. ;)

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