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Monday, June 13, 2016

Another ancient genome from Iran coming soon


Update 14/07/2016: Early Neolithic genomes from the eastern Fertile Crescent (Broushaki et al. 2016)

...

Very interesting abstract here from a recent genomics conference in London. I do have a few more details from this presentation, but I guess they're not yet online for a reason, so let's just wait until the paper comes out. Suffice to say, the data in this paper is going to be very useful in the Proto-Indo-European (PIE) homeland debate. I just hope that the mixture model chosen by the authors is really solid and doesn't leave too much to the imagination.

Iran is considered a pivotal region in the Fertile Crescent, occupying a central space between Africa and Eurasia, and has thus been extensively studied to infer the development of the earliest human civilizations and farming settlements. From a historical and cultural perspective, this region is also of great interest as the cradle of Zoroastrianism. With reported roots dating back to the second millennium BC in Iran, Zoroastrianism is one of the oldest religions in the world and is now mainly concentrated in India, Iran, and Southern Pakistan. In this work we present novel genotype data from present-day Zoroastrians from Iran and India, along with a high coverage (10x) early Neolithic sample from Iran (7,455-7,082 BC), comparing these samples to publicly available genome-wide genotypes from >200 modern and ancient groups worldwide to elucidate patterns of shared ancestry. We apply a novel Bayesian mixture model to represent the DNA from modern and ancient groups or individuals as mixtures of that from other sampled groups or individuals, using a haplotype-based approach that is more powerful than commonly-used algorithms. Our mixture model identifies which sampled groups are most related to one another genetically, reflecting shared common ancestry relative to other groups due to e.g. admixture (i.e. intermixing of genetically distinct groups) or other historical processes. Interestingly, analysis of ancestry patterns revealed strong affinities of the Neolithic Iranian sample to modern-day Pakistani and Indian populations, and particularly to Iranian Zoroastrians, in stark contrast to Neolithic samples from Europe. We also identify, describe and date recent admixture events in modern-day Iranian groups that have altered their current genetic make-up relative to these ancient origins.

Saioa López et al., The genetic landscape of Iran and the legacy of Zoroastrianism: Comparing haplotype sharing patterns among ancient and modern-day samples using a mixture model, poster presentation, Quantitative Genomics 2016, University College London (UCL)

See also...

Neolithic genome from Iran SMBE 2016 teaser

128 comments:

Alberto said...

So now we'll get 2 Early Neolithic Iranian samples? That's great news. From this one they don't say the exact location or even if it's male or female. We'll have to wait for that.

So this sample shows higher haplotype sharing with Zoroastrian Iranians than with non-Zoroastrian ones? I presume that the non-Zoroastrian ones would mostly be Muslim, but would that mean that there was a significant genetic impact with the arrival of Islamism? (Which would be consistent with the last sentence about "recent admixture events" that have altered the genetic make-up of modern day Iranian groups).

Davidski said...

@Alberto

This one is also from western Iran.

So this sample shows higher haplotype sharing with Zoroastrian Iranians than with non-Zoroastrian ones? I presume that the non-Zoroastrian ones would mostly be Muslim, but would that mean that there was a significant genetic impact with the arrival of Islamism? (Which would be consistent with the last sentence about "recent admixture events" that have altered the genetic make-up of modern day Iranian groups).

Maybe, but think also Iron Age.

Roy King said...

Fascinating! It looks like the Iranian Neolithic will cluster with present day Iranians and Pakistanis, hence CHG-like. Also the group that did this study is the same group as those who did the Hofmanova et al study that Davidski objected to so strenuously a few days ago.

aniasi said...

It would not surprise me if Iran's profile was changed by the mass arrival of Turkic peoples beginning in the Middle Ages. Think Seljuks, Ghaznivids, etc.

Also, cue the OIT/IAT theories coming out that this is proof of neolithic continuity. In 5.... 4..... 3.... 2....

Davidski said...

@aniasi

It would not surprise me if Iran's profile was changed by the mass arrival of Turkic peoples beginning in the Middle Ages. Think Seljuks, Ghaznivids, etc.

Yeah, maybe, but the Iron Age came before the Middle Ages.

Also, cue the OIT/IAT theories coming out that this is proof of neolithic continuity. In 5.... 4..... 3.... 2....

Nah, Out of Iran and Out of India proponents are up shit creek without a paddle because of these genomes. You'll see why.

Davidski said...

Here we go, Wikipedia is our friend, at least in this instance anyway...

Early Iron Age Iran

As early as the 20th century BC, tribes came to the Iranian Plateau from the Pontic–Caspian steppe. The arrival of Iranians on the Iranian plateau forced the Elamites to relinquish one area of their empire after another and to take refuge in Elam, Khuzestan and the nearby area, which only then became coterminous with Elam.[35] Bahman Firuzmandi say that the southern Iranians might be intermixed with the Elamite peoples living in the plateau.[36] By the mid-first millennium BC, Medes, Persians, and Parthians populated the Iranian plateau.


https://en.wikipedia.org/wiki/History_of_Iran#Early_Iron_Age

Roy King said...

I agree with Davidski that the Iranian genomes likely will show Neolithic continuity across Western Iran to Pakistan with an Iron Age immigration of Indo-Iranians/Indo-Aryans to the region(s). My guess is that Elamite language was correlated with the long term presence of Neolithic farmers. The radiocarbon dating of this sample to about 7000-7500 BCE is quite early and comparable to Late PPNB in West Asia.

Davidski said...

Indeed, and I'll just quit playing games. They also have an Iron Age genome. Not sure why it's not mentioned in the abstract though?

Iranocentrist said...

@Davidski

Wow an Iron Age sample, so do you already know the results?

Davidski said...

I don't know the details. Just been told that there was a genetic shift during the Iron Age.

Nirjhar007 said...

David,

Do ask the authors to not publish the y-dna.

Yes, its going to great , finally , aDNA from key areas are starting to arrive...

Nirjhar007 said...

Roy,

Steppe Migration of of Aryans and the Hollow Earth theory , falls into the same category...

Iranocentrist said...

@Davidski

"I don't know the details. Just been told that there was a genetic shift during the Iron Age"

Well there you have it then, most of our questions will be answered as pertaining to the IE dispersement in Iran.

Nirjhar007 said...

Iranocentrist,

You can expect some steppe like admixture in the Iron age sample . Its quite likely.

Roy King said...

@Nirjhar007
The Victorian/colonialist model of steppe migration to India doesn't make sense. That said, a shift in the Indus Valley during the Iron Age with incorporation of nomadic/semi-nomadic people does make sense to me. I believe that much of the Vedic religion brought in local elites (ie indigenous Indus Valley castes derived from IVC). We see this evidence in the G-P303 and the J2a-M410 Y chromosomes among the Iyers and Iyengars of Tamil Nadu (as well as R1a1). So the Vedic culture is a hybrid one, ultimately.

Coldmountains said...

I think they were Baluch or Kalash like but without steppe admixture. More EEF-related West Asians migrated to the Caucasus and Iran so modern Caucasians and Iranians are more SW Asian/EEF shifted but this had hardly anything to do with islam and arabs and this "genetic shift" happened in my opinion already before Aryans arrived there.

Nirjhar007 said...

Roy,

There was no shift before the middle of 1st millennium bc. The de-urbanization did happen . But it started to rise again from ~1200 BC , after the effect of climatic change got neutralized. Let the aDNA come . Vedic culture is just one portion ....

Davidski said...

Famous last words.

aniasi said...

@Davidski

There is not citation for the early 20th C BC date there. Also, those late bronze age/iron age migrations would have affected ancestral Indian populations and Zoroastrian populations as well. What would have separated them was the arrival of the Turks.

Also

"Nah, Out of Iran and Out of India proponents are up shit creek without a paddle because of these genomes. You'll see why."

Someone above is still putting it in the same category as flat-earth.

Davidski said...

@aniasi

Most populations from Iran to South India share a lot of genomic tracts and drift with these early Neolithic western Iranian farmers, especially compared to groups from outside the region, and in particular Europeans.

However, some of them, like the more isolated ones, such as the Zoroastrians, have preserved more of the Iranian Neolithic ancestry. They're like the Sardinians in Europe, who are the best proxy for early European and Anatolian farmers, but not the only population in Europe to show high affinity to them.

Like I said, I don't know much about that Iron Age Iranian genome, but we don't have to assume that it's much more similar to Iranians than to Iranian Zoroastrians.

It might be like those Bronze Age Armenian genomes; lots of steppe ancestry compared to modern Armenians that we wouldn't even know existed there without those samples.

However, steppe ancestry is easy to detect in upper caste Indians, especially from north India, as well as Hindu Kush and Pamir Indo-Iranians. So there's also that.

MfA said...

Aren't Zoroastrians in India half way South Indian, especially through maternal line?

Yazidis(Êzidî) are Pagan Kurds, who don't mix outside of their religion. They're just like rest of the Kurds genetically. So we can say post Islam demographics didn't effect the genetic makeup of Kurds, and probably much of the Iran.

aniasi said...

@Davidski

I think we are in agreement on most of this. I suspect this sample may become the equivalent of an "Early Anatolian Farmer" for Indian and Iranian (maybe South Central Asian) populations.

I also wonder if we might find another component, a pre-CHG (or CHG-like) population in the plateau.

Nirjhar007 said...

Just one thing , Zoroastrians are a directly related group of the Aryans . Of course there were admixtures, but the fact I mentioned, should always be remembered.

Coldmountains said...

@Nirjhar

They are genetically and culturally quite different from Aryans and not closer to theM than other modern day Indo-Iranians.
They tend to be very low in R1a and have rather low steppe affinity. Zoroastranism is a post-Aryan religion and shows strong Pre-Aryan influences. It developed in BMACized East Iranic communities and later spread to West Iran. Vedic Hinduism is much closer to Proto-Aryan religion and Brahmins preserved better steppe ancestry

Nirjhar007 said...

CM,

Their religion was a result of a new ideology, they reformed the old doctrine . But they are still three thousand five hundred year old !. They also influenced Judaism and Christianity clearly! . I don't know , which ''Pre-Aryan''traits you are talking about .

Gökhan said...

I agree with Nirjhar007 that Zoroastrians directly related with proto-aryans who occupied Iranian Platue and brought indo-iranian languages to region. On the other hand i suppose that there were several indo-european step invasion toward Iranian platue. Probably first ones were R1b and rest were R1a dominated. (Medians and Parthians probably were the members of second one)

Nirjhar007 said...

I think Gokhan , the age of that Iron Age sample is very significant . I think , it should be post 1000 BC ..

Jijnasu said...

Very interesting. However have to say that the idea that Zoroastrians some how represent the Neolithic population better because they're currently isolated seems strange to me. There isolation probably began only following the islamisation of Iran. Pre-islamic persians were predominantly Zoroastrian and the religious tradition had a significant following amongst other iranic peoples too. Also zoroastrianism derives from early indo-iranian religion with some near eastern influences

Jijnasu said...

Another point to be noted is that zoroastrianism arose in bactria among an east iranic speaking people.The western iranic persians and medes who occupied much of what is now iran aren't attested until the early first millenium BCE

Onur said...

@MfA

Aren't Zoroastrians in India half way South Indian, especially through maternal line?

Yazidis(Êzidî) are Pagan Kurds, who don't mix outside of their religion. They're just like rest of the Kurds genetically. So we can say post Islam demographics didn't effect the genetic makeup of Kurds, and probably much of the Iran.


I completely agree with your points, MfA. Also, since this paper is the work of the same team as the one who did the Hofmanova et al. paper, we should not expect much accuracy in their conclusions.

Coldmountains said...

The reason why Zoroastrians are closer to Neolithic Iranians is probably their higher CHG/EEF ratio compared to other Iranians but despite their South Asian admixture they are not really very different from other modern day Iranians and show also SW Asian//EEF admixture just a bit less than other because they got some South Asian ancestry on their maternal side. I think the Neolithic Iranians will be similar to the non-steppe part of Pashtuns and other East Iranics with high CHG

Jijnasu said...

But I think their talking about iranian Zoroastrians not Indian Zoroastrians ie Parsis who have south asian maternal ancestry

Nirjhar007 said...

Dr. Saioa López,

If you don't mind . What is the C14 date, of the Iron age Iranian sample?.

Onur said...

@Coldmountains

The reason why Zoroastrians are closer to Neolithic Iranians is probably their higher CHG/EEF ratio compared to other Iranians but despite their South Asian admixture they are not really very different from other modern day Iranians and show also SW Asian//EEF admixture just a bit less than other because they got some South Asian ancestry on their maternal side.

Only Zoroastrians of South Asia have recent South Asian admixture (almost totally on their maternal side). Zoroastrians of Iran do not have any recent South Asian admixture, and I think they are genetically very similar to Muslim Iranians just as Yazidi (Ezidi) Kurds are genetically indistinguishable from Muslim Kurds.

Nirjhar007 said...

People remember :

Interestingly, analysis of ancestry patterns revealed strong affinities of the Neolithic Iranian sample to modern-day Pakistani and Indian populations, and particularly to Iranian Zoroastrians, in stark contrast to Neolithic samples from Europe.

They speak of Iranian Zoroastrians , Not the ones from India .

Onur said...

They speak of Iranian Zoroastrians , Not the ones from India .

I noticed that, Nirjhar.

Onur said...

@aniasi

It would not surprise me if Iran's profile was changed by the mass arrival of Turkic peoples beginning in the Middle Ages. Think Seljuks, Ghaznivids, etc.

The genetic impact of the Turkic invasion of Iran is almost totally restricted to the Turkic-speaking parts of Iran.

Alberto said...

Difficult to know what they mean by Iranian Zoroastrians. But I don't think this group is well sampled or that it's similar to people from Pakistan and India. So probably it's another ambiguous term referring to Zoroastrians from Iranian origin, but living in India today (though who knows, maybe they really mean Zoroastrians from Iran).

So Neolithic Iranians were more similar to modern day Pakistanis than to modern day Iranians. And what's the main difference between Pakistanis and Iranians? I would say that Pakistanis have more ANE and more ASI, while Iranians more Anatolia_Neolithic. This would mean that what characterized this Neolithic sample was high ANE (and maybe ASI?) and low Anatolia_Neolithic. And that West Asian migrations (Iron Age and/or later) diluted this affinity in modern day Iranians (but less so in modern day Pakistanis and Indians).

Or...? Or maybe I'm just reading too much into an abstract.

Atriðr said...

Good stuff.

This falls in line with what I mentioned about Iranic languages in another post.

Achaeamenids will be shown to be elite w/Steppe, built on Elamite civilization... which itself may have some direct or indirect link with IVC.

Sanskrit older than Avestan, but turning out that Avestan Airyanem Vaejah was pretty accurate.

@Davidski any dates when this comes out? Any hints on their Y-haplos? If no R1a1a, then that will be quite interesting too.

Atriðr said...

@Alberto

I interpreted as referring to historical Zoroastrians (in Persia) and less to the Parsis in India (who escaped to India after the fall of the Sassanians).

Kurds/Yazidis likely connected to original Zoroastrians as well, who had to modify beliefs in accordance to new religious eco-system. Maybe these are the Iranians meant.

Onur said...

@Alberto

So probably it's another ambiguous term referring to Zoroastrians from Iranian origin, but living in India today (though who knows, maybe they really mean Zoroastrians from Iran).

In the abstract they use these statements: "In this work we present novel genotype data from present-day Zoroastrians from Iran and India" and "Interestingly, analysis of ancestry patterns revealed strong affinities of the Neolithic Iranian sample to modern-day Pakistani and Indian populations, and particularly to Iranian Zoroastrians". In the first one they refer to Iran and India and in the second one they only refer to Iran when talking about Zoroastrians. Why would they omit the reference to India in the second statement if they were referring to Zoroastrians from India in that one?

Ariele Iacopo Maggi said...

The out of India theory does not exist in the data. European are 0% indian, how that came to be if IE came from India? The only alternative is the iranian plateu CHG=IE theory, but as you all already know in a recent paper they found that pre agricultural Iran had no genetic impact on Europe. I mean, Indians are 50% steppe, and Europe and ancient steppe is 0% indian, no gene flow from ancient Iran to Europe either, no impact of EF in India to speak of. It's not even an Ockham's razor situation, it's just that any other theory is physicacly impossible and confirmed not true if you stand by the data.

postneo said...

" I presume that the non-Zoroastrian ones would mostly be Muslim, but would that mean that there was a significant genetic impact with the arrival of Islamism?"

zoroastrians and parsis are an isolated and endogamous minority so they are good population to study as vs mainstream muslim iranians

tew said...

@ "the idea that Zoroastrians somehow represent the Neolithic population better because they're currently isolated seems strange to me. There isolation probably began only following the islamisation of Iran."

But why did those particular populations preserve Zoroastrianism while society at large adopted Islam? Most likely, because their ancestors were already geographically/culturally/linguistically isolated to begin with (even before the arrival of Islam, in relation to other Zoroastrians), so it makes sense that they would retain a more ancient genetic profile. That's the point.

Alberto said...

@Onur

True, I missed that part about newly genotyped data from present day Zoroastrians from Iran. Where do these groups live nowadays (or better, where have they lived historically?). Are they closer to Pakistanis/Indians than to modern Iranians?

Iranocentrist said...

The first mistake in the abstract is mentioning Zoroastrians in Pakistan, which I believe the numbers to be negligible.

The mystery though, is in where Davidski highlighted " Interestingly, analysis of ancestry patterns revealed strong affinities of the Neolithic Iranian sample to modern-day Pakistani and Indian populations, and particularly to Iranian Zoroastrians, in stark contrast to Neolithic samples from Europe."

Are they talking about genotyped modern Pakistani and Indian Zoroastrian populations only or other ethnic groups as well i those respective countries. But they are emphasizing the relatedness of Iranians Zoroastrians to the neolithic Iranian, this I believe leaves us with teo possible scenarios, in no particular order:

Scenario 1. That this neolithic Iranian was part of the Neolithic community stretching from the Zagros all the way to the indus, a predominantly J2 CHG with elevated ANE, that will eventually lead to the Elamite/Jiroft/IVC belt of civilizations, with later Steppe R1a input via Indo-Iranian/Aryan invasions. Since it is pretty clear that Iranian Zoroastrians experienced only minor admixture following the Islamization of Iran, however if we are to go by this first scenario then we should assume that The pre-Islamic Iranians were a hybrid population of Steppe and Neolithic, probably more contribution from the latter as this paper is explicitly stating the relationship between Iranian Zoroastrians and the Neolithic Iranian.

Scenario 2. That Ancestral to Z93 would be found amongst the Neolithic Iranian sample/s, where a small few paternal lines left for the steppe and founded the Sintashta/Andronovo/CW, through mixing with European types, I say a small few because there is, I believe though could be wrong, a small amount of the Gedrosia component in most European modern and BA samples and that could the legacy of these Iranian Plateau R1a men. Most will probably find the second scenario laughable, but if it's not the fist scenario then I can't think of anything other then the second.

Sorry for the long post

Onur said...

@Alberto

True, I missed that part about newly genotyped data from present day Zoroastrians from Iran. Where do these groups live nowadays (or better, where have they lived historically?)

On modern Zoroastrians of Iran, take a look at this article:

https://en.wikipedia.org/wiki/Zoroastrians_in_Iran

Are they closer to Pakistanis/Indians than to modern Iranians?

Of course they are not. What kind of a question is that?

Rami said...

I am more interested in the Neolithic sample results, but it makes no sense a modern Iranian Zoroastrian would be similar to the Neolithic one considering modern day Iranian Zoroastrians are quite similar to other Iranians, they have too much EEF for that. Baloch, Brahui, and Kalash(minus their steppe) seem better fits.
At some point there was a massive shift in the population in Iran which brought Neolithic Anatolian Farmers who displaced and absorbed the local CHG like population.

Kurd said...

The one Zoroastrian modern sample from India that I had analyzed was more similar to Iranians and Kurds than to Gujaratis from the area in India where this individual is from. I am not sure what the variation is among Indian Zoroastrians, but if this individual was representative of other Zoroastrians in India, that would mean that the Zoroastrians of India have done an amazing job preserving their gene pool after living in India for 1000 years. The other thing I seem to remember is that it was quite a bit less steppe shifted than SC Asians.

Onur said...

Also on modern Zoroastrians of Iran:

"Zoroastrians mainly are ethnic Persians and are concentrated in the cities of Tehran, Kerman, and Yazd. The Islamic Republic government estimates the number of Zoroastrians is 20,000, Zoroastrian groups in Iran say their number is approximately 60,000.[4] According to the Iranian census data from 2011 the number of Zoroastrians in Iran was 25,271.[120]"

https://en.wikipedia.org/wiki/Religion_in_Iran#Zoroastrianism

capra internetensis said...

Encyclopedia Iranica has lots on Iranian Zoroastrians

Zoroastrians in Iran

They still do the soma ritual, using ephedra - or at least they did a hundred years ago.

(Oooh, there's an abstract of a study on the Democratic Republic of Congo - 788 individuals from 29 populations at 250k SNPs. Yay!)

Roy King said...

Grugni et al (2012) in PLoS ONE genotyped Iranian which included Zoroastrians from Yadz and from Tehran. What both groups showed was increased J2a4h-L24 (17.6% and 15.4 % respectively). The Yadz Zoroastrians had 17.6% R1a1 while the Tehran Zoroastrians had M269*(xL23) at 15.4%. My guess is that the J2a4h's reflect the increased correspondence between Neolithic Iran and the Zoroastrians via autosomal DNA.

Rami said...

@ Kurd
Indian Zoroastrians are a bit more South Asian shifted versions of their Iranian brethren and yes for the most part they are endogamous, but significant amount of the Parsee population descend from relatively recent migrants from Iran, who came in the 18/19th centuries

Davidski said...

Modern Persians also share a lot of ancestry with the early Neolithic Zagros samples. It's not like Zoroastrians do and other Persians don't; they both do.

Onur said...

@capra

Encyclopedia Iranica has lots on Iranian Zoroastrians

Zoroastrians in Iran

They still do the soma ritual, using ephedra - or at least they did a hundred years ago.


Encyclopedia Iranica is a good source of info on Iran and Iranian peoples, which I sometimes make use of. Thanks for sharing that.

Onur said...

@Davidski

Modern Persians also share a lot of ancestry with the early Neolithic Zagros samples. It's not like Zoroastrians do and other Persians don't; they both do.

Exactly

Rami said...

Obviously they will have Zagros ancestry David, duh. But there was massive influx of Anatolian Farmers into the region at some point . One thing is clear Neolithic Iran and Neolithic South Asia seem to be closely connected at some point

postneo said...

"They are genetically and culturally quite different from Aryans and not closer to theM than other modern day Indo-Iranians."

Thats not correct. parsis and zorastrians have preserved the gathas whose language is closed to vedic in morphology. They just cannot fake this. since they are geographically quite far away from brahmins of india and have not had cultural contact for at least 3000 years according to the mainstream. The only memory they have is of being lost enemies. The word Arya itself is inherited from the gathas and vedic/indic cultural context. Other representations are artificial. so if Zoroastrians are not Arya, then no one is...

By saying parsis are not aryan because they don't have high amounts of R1a is like the tail trying to wag the dog. R1a is inconsequential to being Aryan. Indo aryans just happen to be strongly correlated to R1a but that may not be true of other Aryas.

aniasi said...

@ Tew

Religious conversion can often happen for socio-political reasons. Zoroastrians in Iran are not isolated to remote areas. They simply were more fortunate in being able to hold on to their religion, and do not show much in the way of caste endogamy.

@ Kurd

That sample is likely an Irani. While Parsis arrived in the early middle ages, the Iranis were Iranian Zoroastrians who arrived in the 18th and 19th century due to Qajar persecution, with the aid of the Parsis.

postneo said...

"that would mean that the Zoroastrians of India have done an amazing job preserving their gene pool after living in India for 1000 years."

I grew up in bombay and know many parsis. They have done a somewhat amazing job even to their detriment. They are helped by the fact that most communities in India are endogamous. Last I heard their population is dwindling. One sometimes hears directives/articles for parsis to go forth and breed, marry outside etc for health reasons.

Kurd Dgk said...

I don't see how an early Neolithic sample can be more ancestral to Baloch to the exclusion of Kurds and a couple of other Caucausus based groups, when Baloch did not even exist as their own separate group back then.

Many Baloch are nothing more than Kurds with a bit of added recent S Asian admixture (probably 1000-2000 years ago).

The genetic similarity between Kurds and some Baloch individuals using dstats and qpAdm suggests a relatively recent migration of Baloch from the NW Iran area.

Therefore an early Neolithic sample should in theory be equally ancestral to Baloch Kurds and other Iranian groups, since many of these had not split from each other yet that long ago.

One factor that can make one Iranian group more similar to the Neolithic sample than others, is if the group has experienced less non Neolithic Iranian admixture than the rest, perhaps due to the group's isolation (zoroastrians maybe). If Baloch due end up a little more similar, it would not be due them having more direct ancestry from NI but rather due them not experiencing as much non NI admixture subsequent to their migration from NW Iran area

Davidski said...

By the way, these Zagros farmers are the most Basal Eurasian samples sequenced to date.

So I'm wondering if the pseudo-Sub-Saharan signal that shows up in some of my tests, like the ANE K8 and Yamnaya K6, in South Asians isn't due to the algorithm compensating for a lack of a proper cluster for this very basal admixture?

Roy King said...

@Kurd Dgk
Another group that should also have connection to these Zagros Neolithic samples is Assyrians. Assyrians, in general lack much Arab admixture historically and speak a Semitic Language--Aramaic. As such, they might have less steppe admixture than say modern Iranians.

Davidski said...

Assyrians have too much Anatolia Neolithic ancestry.

For these Zagros farmers, think Brahui minus Ancestral South Indian (ASI) or Sub-Saharan admix.

Roy King said...

@Davidski,
We know that South Asians (and South Iranians) had major interactions and population exchanges with East Africa, even in recent times. Is the Sub-Saharan ancestry in South Asians explicable through these interactions?

Davidski said...

Not sure. It mostly looks very recent, especially in the Makrani. So I'd say that the Balochs and Brahuis with clear levels of SSA are probably part Makrani. But some of the SSA across South Asia might be older.

However, all South Asians score some SSA in some of my tests, even though most shouldn't, as they don't show any in tests specifically designed to pick up SSA. So I suspect this signal is caused by their excess Basal Eurasian from Neolithic Iran.

Onur said...

@Davidski

However, all South Asians score some SSA in some of my tests, even though most shouldn't, as they don't show any in tests specifically designed to pick up SSA. So I suspect this signal is caused by their excess Basal Eurasian from Neolithic Iran.

Is the SSA in South Asians correlated with ASI? If so, it may be because of ASI ancestry rather than Basal Eurasian.

Roy King said...

@Davidski
"Assyrians have too much Anatolia Neolithic ancestry.
For these Zagros farmers, think Brahui minus Ancestral South Indian (ASI) or Sub-Saharan admix."
Thanks! So there is a border, approximately between present day Iraq/Turkey and Iran, that separates modern populations that cluster with the Zagros Neolithic samples from those modern populations, like Assyrians, who have a large Anatolian Neolithic component. Perhaps this border separates the PPNB Neolithic from the Zarzian Neolithic derived populations.

Davidski said...

Pretty much. The Zagros Neolithic ancestry apparently drops like a rock west of Iraq and northwest of Iran.

Onur said...

As an additional note to my previous comment, South Asia is not a particularly Basal Eurasian-rich region. West Asia has higher Basal Eurasian than South Asia and in South Asia ASI and Basal Eurasian are inversely proportional.

Davidski said...

The Zagros farmers are CHG-like, but apparently they're easily the most Basal Eurasian population known at this stage, and they contributed a lot of ancestry to South Asians.

So if you take out the Ancestral South Indian (ASI) and steppe-derived admixtures from South Asia, you're basically left with the very Basal Eurasian Zagros admixture.

Iranocentrist said...

Davidski since you have so much insider info, can you state when the paper will be published? Thanks in advance

Onur said...

@Davidski

So if you take out the Ancestral South Indian (ASI) and steppe-derived admixtures from South Asia, you're basically left with the very Basal Eurasian Zagros admixture.

Yes, it is the CHG-like part of the ancestry of South Asians that is particularly Basal Eurasian-rich. That is why Baloch and Brahui are so Basal Eurasian-rich and Paniya and Pulliyar are so low on Basal Eurasian.

Rob said...

Dave

"Pretty much. The Zagros Neolithic ancestry apparently drops like a rock west of Iraq and northwest of Iran"

This must relate to impact of recent Arab expansions , although Mesopotamia was apparently poorly inhabited going into the Holocene, so some of this structure is probably even more archaic

For the king said...

aniasi said...

" @ Kurd

That sample is likely an Irani. While Parsis arrived in the early middle ages, the Iranis were Iranian Zoroastrians who arrived in the 18th and 19th century due to Qajar persecution, with the aid of the Parsis. "

No, that sample is Parsi. The person clearly stated that they were from the Parsi community, not the Irani community. Marriage between those different Zoroastrian communities is rare in south Asia.

For the king said...

Rob said...
" Dave

"Pretty much. The Zagros Neolithic ancestry apparently drops like a rock west of Iraq and northwest of Iran"

This must relate to impact of recent Arab expansions , although Mesopotamia was apparently poorly inhabited going into the Holocene, so some of this structure is probably even more archaic. "

Modern non Iranic Mesopotamians are fairly close to Iranians and Kurds, including the Muslim Arabs. Only Tribal Iraqi Arabs show significant Arabian admixture. I'd guess the rest of Iraqis should have a lot of Zagros Neolithic as well.

Davidski said...

@Iranocentrist

No idea. You should e-mail the authors and ask. They probably won't talk to me after my recent blog posts and comments. :p

@Rob

The Anatolian farmer/Zagros farmer divide looks like a really old phenomenon, although it might have shifted a bit here and there, considering the significant Anatolian input into modern Iranians. Some of this, however, actually came from the steppe along with EHG and CHG proper, as part of the early Iranian expansions of the Srubnaya and related groups.

Indeed, it's interesting that Zagros affinity has remained high in South Central Asia despite recent Arabian gene flow into many parts of the region.

Rob said...

@ Dave, and FTK

Ok then. That would make sense. As I said, based on current spatial maps, the Kabaran- Natufian and Zarzian appear geographically separated by a large patch of 'no-mans-land' during the LUP (although some of this might be research related).

aniasi said...

Wait... I'm really confused now.

I thought basal eurasian was paleolithic, concentrated in SW Asians (bedouin) and not found in South Asia. I have clearly missed a lot. Can you fill me in?

Davidski said...

@Rob

The no man's land is probably the area where affinity to both EEF and Zagros farmers is low, and more or less even. I suspect this is caused by a third type of Neolithic ancestry, as well as some Arabian and Sub-Saharan admixture, in the Levant, and CHG and European admixture in the Caucasus.

In other words, this area is basically the border between EEF and Zagros farmers, but yeah, there are also other things going on there.

@aniasi

All populations with significant West Eurasian or Caucasoid ancestry have some Basal Eurasian admixture, all the way from Iceland to South India. That's because Basal Eurasian admixture expanded in a major way out of the Fertile Crescent along with early farmers and the Neolithic package during the Neolithic, and this is the process that created the West Eurasian biogeographic zone, or Caucasian race if you will.

K U. said...

The fact that the paper specifically mentions the affinity towards Pakistanis, Indians, and Zoroastrians instead of modern "typical" (ie, Persian Muslim) Iranians implies this Neolithic Iranian had a higher Ancestral South Indian component than the modern Iranian mean, no?

Davidski said...

Well, the Neolithic genome does generally show high affinity to Muslim Persians. This is not in the abstract but I can assure you that it does.

postneo said...

"Indeed, it's interesting that Zagros affinity has remained high in South Central Asia despite recent Arabian gene flow into many parts of the region."

Arab gene flow is not expected to be much due to known history.

Islamic expansion into the subcontinent happened more from central asia. The initial arab campaigns in sindh did not have much impact. Lasting conquests were initiated by "turkic salve dynasties and mongols" and came from areas such as southern kazakhistan , northern afghanistan and later uzbegistan ( turko mongol).

so the arabs conquered persia first and then the turks and mongols islamized and persianized them selves before before ruling the sub continent. This makes sense geographically too.

Davidski said...

Many of the Balochi, Brahui, and Makrani samples from the HGDP that I have show clear Bedouin-like and Sub-Saharan admixtures. Even the Punjabis from Lahore from the 1000 Genomes show some of this influence. So this type of ancestry has made a significant impact in Pakistan, unless the pedigrees of these individuals are somewhat unusual. But I doubt it.

Coldmountains said...

@Davidski

Arabs had no significant genetic impact anywhere east of Iraq. Even in West Iran there was hardly any Arab gene flow. Arab deep Y-DNA clades are absent in South Central Asia and South Asia and even the people who claim arab ancestry there are mostly just locals. Actually there was South Asian and Central Asian gene flow into Arabia so that some Arabs have significant amounts of Central and South Asian Y-DNA. The only recent West Asian migration which had some genetic impact in South Central Asia was the migration of Persians into Central Asia.

The reason why Baluch and Iranians score SW Asian/Bedouin like admixture is in my opinion Pre-Indo-Iranian genetic diffusion from the west which probably brought both EEF and SW Asian admixture to the region

Davidski said...

The reason why Baluch and Iranians score SW Asian/Bedouin like admixture is in my opinion Pre-Indo-Iranian genetic diffusion from the west which probably brought both EEF and SW Asian admixture to the region.

Impossible. It's too uneven. It would be much more even if it was ancient. And it's often accompanied by really high levels of Sub-Saharan ancestry, which again should be more even if ancient.

There's obviously been quite a bit of gene flow from Arabia and East Africa to the Makrani coast area, probably from slaves and Arab slave owners, and this has recently diffused into other parts of Pakistan.

Coldmountains said...

@Davidski

Ok the Makrani coast is maybe an exception (SSA Ancestry is mainly from Africans there and not from Arabs) but talking about Afghanistan, Central Asia and most of Iran there is not much with points to recent arab or other SW Asian ancestry there. SW Asian ancestry there is not the same like arab ancestry and there was a genetic shift in Iran long before and the same genetic shift happened in the Caucasus. Muslims not caused this genetic shift because Pre-Muslim or Christian groups of the Caucasus and Iran are very close to their muslim neighbours

Gökhan said...

If this Neoletihic sample from Iran is CHG-like, i would expect similarities between georgians but not Indians or Pakistanis. Why authors just focused on modern Zoroastrians, Indians and Pakistanis while we know that the most CHG like modern samples are Georgians, Megrelians and other Southern caucaus populations? In my opinion that samples should be analaysed independently from the upcoming article.

Samuel Andrews said...

Looking at mtDNA and Y DNA it looks like there's been gene flow between Iran, SC Asia, and SW Asia. Either SW Asians have ancestry from people like the ones who lived in Neolithic Iran or modern Iranians and SC Asians have ancestry from SW Asia.

@Gokhan,
"If this Neoletihic sample from Iran is CHG-like, i would expect similarities between georgians but not Indians or Pakistanis."

Neolithic Iranians were similar to CHG but not CHG. Relatedness to Neolithic Iranians isn't determined by how much CHG ancestry you have. And Neolithic Iranians are probably more directly ancestral to modern Iranians and SC Asians than they're to Caucasians.

Davidski said...

The Zagros farmers are relatively most similar to CHG, but more Basal Eurasian than them, and certainly not the same population. So what's the issue here?

As you can see in the abstract, the authors tested over 200 populations, including Caucasians. Obviously, Georgians didn't exactly light up the analysis, otherwise they'd get a mention.

George Okromchedlishvili said...

Georgians have quite a lot of ENF admixture.
And it's my personal belief that Kartvelian language family ultimately derives from something like Natufians.

postneo said...

a corollary of this: Zoroastrians are probably not a homogenous population and different groups may serve as good time/space capsules of Iranian genetics.

Seinundzeit said...

For me, the most radical implication here seems to be that the peoples of Balochistan (the Brahui and Baloch/Makrani) are basically the Sardinians of Iran/Central Asia/South Asia.

Obviously, they do have some Arab-related admixture (the Baloch have longstanding commercial/cultural connections with the Arabian peninsula), and they probably have some very minor steppe admixture (not to mention perhaps a slight amount of ENA/or whatever ancient South Asian hunter gatherers were, hopefully those questions concerning South Asia are soon to be resolved as well), which would distinguish them from these ancient Iranian genomes.

But I'm pretty sure that, at the end of the day, they are around 80%-90% genetically derived from Neolithic Iranian plateau populations. Just like how Sardinians are also 80%-90% genetically derived from Neolithic Anatolian plateau populations, but modified by 20%-10% WHG (and perhaps very minor steppe-related admixture is also included in that 20%-10%).

With that in mind, I played around with the nMonte sheets. Basically, I tried to model the Brahui, using "basal" populations (ANE, WHG, Basal Eurasian, etc), since this is a population that is overwhelmingly Zagros Neolithic in terms of genetic ancestry, and since I just want a very broad idea of how those Iranian genomes will stack up.

Obviously, David will be able to do amazing things (as he can now use qpGraph), once he gets the Iranian samples. So this is only meant as a very rough preview/broad brush outline of what we'll probably see, nothing more.

PCA nMonte
66.95% ANE (MA1)
27.70% Basal Eurasian (Alberto's PCA-based Basal Eurasian ghost)
4.40% ENA
0.95% Sub-Saharan African

D-stats nMonte
34.38% ANE (MA1 + Afontova Gora3)
33.00% Basal Eurasian (Matt's "Basal_Sim2")
22.90% Kostenki14 (I suppose this is indicative of unidentified West Eurasian ancestry)
7.30% ENA
1.95% UHG (Matt's "SimulatedUHG1")

D-stats nMonte (different sheet, has Onge)
37.15% ANE (MA1)
31.35% Basal Eurasian (I created this myself, it worked well)
17.20% Western HG (Loschbour)
11.7% ENA
2.60% Sub-Saharan African

Compared to CHG:

PCA nMonte
56.15% ANE
31.40% Basal Eurasian
11.00% WHG
1.45% Yoruba

Brahui/Baloch seem more ANE-admixed, and have no affinity to WHG, compared to CHG.

But again, I wouldn't take this too seriously. Once David has the actual Iranian genomes, and starts working with qpGraph, much will be answered. Can't wait to see the papers, exciting times.

Samuel Andrews said...

@Sein,

Why are you so confident Brahui/Baloch are 80-90% Neolithic Iranian? Also Sardinians are not 80-90% Neolithic Anatolian but they might be 80% Neolithic European(but probably less than that). They don't have a significant amount of Steppe admixture but they have a significant amount of SW Asian ancestry like all Southern Europeans(except Basque).


Seinundzeit said...

Quite a few factors. For one, the authors have stated that this Zagros Neolithic component peaks in Balochistan and South India (see Anthrogenica for details, a poster seems to have spoken to them), so that is a very huge tell. In fact, the authors' claim in this regard is pretty huge.

But even ignoring that, there have been many indications, for a very long time. For example, a simple IBS-based PCA tends to cluster Satsurblia/Kotias with the Brahui/Baloch, while other South Central Asians deviate from the Brahui/Baloch in both a South Asian and a northern European direction. That seemed strange, but is easily explicable now, if the Brahui/Baloch are overwhelmingly derived from a population that was CHG-like (Neolithic Iranian plateau populations), and other South Central Asians are derived from the same complex of groups, but with both BA steppe and South Asian hunter gatherer admixture.

Also, David had a very solid TreeMix run which had a Brahui migration edge into the root of Indian populations, followed by a very substantial BA steppe migration into upper caste North Indians. So in that experiment, the Brahui acted as a proxy for the West Eurasian admixture shared between southern and northern India, which brings us back to the information contained in this abstract concerning the important links between this Neolithic Iranian and Pakistani/Indian populations.

On top of that, the Brahui speak a Dravidian language, which brings to mind the whole Elamo-Dravidian notion, which brings us back to the ancient roots of the Brahui/Baloch on the Iranian plateau (although, it goes without saying that Balochistan is technically a part of the Iranian plateau).

Finally, anyone who has been to Balochistan can tell you that it is an exceedingly isolated region, shockingly cut off from the rest of Pakistan/Afghanistan/Iran. If one is looking for people who have preserved this Neolithic Iranian ancestry to the fullest extent, greater Balochistan is certainly one of the best places to look. There is a reason that a Dravidian language still flourishes here.

Also, when it comes to Sardinians, that is basically nitpicking/splitting hairs. Neolithic Europeans like the Starcevo_EN sample, or even Stuttgart, are pretty close to being almost 100% Neolithic Anatolian in terms of genetic ancestry, allowing for genetic structure in Neolithic Anatolia. So, saying that Sardinians are 80%-90% Neolithic European is basically equivalent to saying that they are 80%-90% Neolithic Anatolian.

Kurti said...

said MFA
"Yazidis(Êzidî) are Pagan Kurds, who don't mix outside of their religion. They're just like rest of the Kurds genetically. So we can say post Islam demographics didn't effect the genetic makeup of Kurds, and probably much of the Iran."

Exactly I have been saying this, I think pre Islamic Semitic groups played a much bigger role than post once. For example we have quite some evidences of admixing with Assyrians, Babylonians, Aramaens who were probably very Levantine like until they merged with the CHG like Sumerians, Hurrians and West Iranics.

Kurti said...

Zoroastrianism ultimately evolved out of a Proto Iranic religion of sun worshipping. This religion in West Iran fusioned with Sumerian planet cult and the Proto West Iranic Mithraism evolved, Mithaism with Anahita, Varna, Ahura Mazda. Previously Ahura Mazda was just one of many Gods and the highest among the West Iranic Mithraists was Mithra himself and was the personification of the sun.

Later the Zoroastrians evolved out of a Mithraistic caste and Ahura Mazda took the position of Mithras as the highest deity for them.

For more information.
https://www.youtube.com/watch?v=0wn623TlM98


With other words Zoroastrianism is actually a quite young religion in comparison to other Iranic once and evolved out of a proto form of Mithraism.

Kurti said...

On the rock reliefes in Taq e Bostan you see Shapur depicted next to two deities, one is Ahura Mazda and the other is Mithras with his head being covered by sun shine. Actually until the Sassanid period Ahura Mazda and Zoroastrianism was never the main religion of the Iranic dynasties. Even during Cyrus Achaemenid reign most people still were kinda Mithraistic. Parthians were Mithraistic visible on the names of the early kings such as Mithridates.

Kurti said...

Alberto said

"So Neolithic Iranians were more similar to modern day Pakistanis than to modern day Iranians. And what's the main difference between Pakistanis and Iranians? I would say that Pakistanis have more ANE and more ASI, while Iranians more Anatolia_Neolithic. This would mean that what characterized this Neolithic sample was high ANE (and maybe ASI?) and low Anatolia_Neolithic. And that West Asian migrations (Iron Age and/or later) diluted this affinity in modern day Iranians (but less so in modern day Pakistanis and Indians)."

The way it sounds to me is, those Iranian Neolithics showa genetic signature that effected both the Iranian Plateau and South Asia. This is something very CHG like. And the reason why they differ slightly from modern Iranians is because those have Anatolian_Farmer admixture. I assume the Iranian Plateau farmers will resemble the West Eurasian genes in Pakistanis minus most of the ASI. Basically a more ANE shifted (gedrosia like? in comparison to Caucasus like in the terms of old calculators) CHG.

Davidski said...

The Zagros farmers are apparently more Basal Eurasian than CHG.

Another difference that we'll probably see between them is Villabruna-related input into CHG, but not into the Zagros farmers.

I doubt the Zagros farmers have any ANE per se. They probably have a related component that will be hard to characterize without more hunter-gatherer samples from all over Central Asia.

Rob said...

@ Sam Andrews

'Sardinians .... have a significant amount of Steppe admixture but they have a significant amount of SW Asian ancestry like all Southern Europeans(except Basque)."

Not that much, really.
SWA admixture barely reaches more than 10% even in southern Greece or parts of Spain. In Sardinians it is ~ 7%, who are otherwise 70 % middle Neolithic Europeans, and some extra (15%) CHG arriving at some point after the Copper Age.
So Sein's statement is on par.

Samuel Andrews said...

@Rob,

Where are you getting those numbers? Everything in Europe which is non-Neolithic and non-Steppe is not mostly CHG. CHG isn't the new non-Steppe admixture that came into Southern Europe after Neolithic, SW Asian is. This has been obvious to me for years now.

How else can you explain the high amounts of Y DNA E1b and J2 in Southern Europe? With the little mtDNA data I have I can already see typical SW Asian mtDNA in Southern Europe as well.

Samuel Andrews said...

What's clear from D-stats is Sardinians are not 100% Neolithic European, they have little or no CHG ancestry, and that they have little or no Steppe ancestry. They fit well as EEF+SW Asian in D-stats.

Rob said...

@ Sam

"Where are you getting those numbers? Everything in Europe which is non-Neolithic and non-Steppe is not mostly CHG. CHG isn't the new non-Steppe admixture that came into Southern Europe after Neolithic, SW Asian is. This has been obvious to me for years now."

-> The ones on the Eurogenes CHG K10 posted on this blog. In it , CHG and SWA are separate components. The latter is very low

" How else can you explain the high amounts of Y DNA E1b and J2 in Southern Europe? With the little mtDNA data I have I can already see typical SW Asian mtDNA in Southern Europe as well. "

This has been explained to you several times. J2 most clearly correlates with the CHG component which arrived to Europe *independent of steppic* stuff. Sure it might have had SWA with it, but clearly its a minor component. Most modern SWA Y haplogroups are J1, not J2, and not the j2b which predominates in Mediterranean Europe.
Also, hg E in Europe came in the Neolithic. E-V13 has been found in Neolithic spain and Hungary. This is all old news.

Samuel Andrews said...

@Rob,

Score in ADMIXTURE component geographic names don't tell you what percentage of ancestry people have from those regions. The "North European" component for example in old Dodecade calculators peaked at just over 50% in Lithaunains, but obvisouly that doesn't mean they are only 50% "North European".

People in SW Asia don't score 100% in the "SW Asia" component. If you modeled South Europeans as a mixture of ancient Europeans and modern Asians, I guarantee you they'd come out as 20-40% SW Asian(Cypriot, Druze, Syrian, etc).

D-stats strongly reject the idea South Europeans have a lot of CHG ancestry. Instead they are modelled best as 20-40% SW Asian. West Eurasia PCAs say the samething and every ADMIXTURE test I've looked into says the same.

"Most modern SWA Y haplogroups are J1, not J2, and not the j2b which predominates in Mediterranean Europe.
Also, hg E in Europe came in the Neolithic. E-V13 has been found in Neolithic spain and Hungary. This is all old news. "

E-V13 existed in Neolithic Europe but was very rare. E-V13 in modern Southern Europe is not of mostly EEF origin. J2a is more popular in Southern Europe than J2b. J2b is only popular in the Balkans, and still J2a is more popular.

Rob said...

yes I'm aware that names are heuristic and not real ancient populations. For illustrations sake, lets look at an Albanian average:

35 % ENF, 30% CHG; 5 % EHG; 15% WHG; 7% 'southwest Asian'


Let's look at Spain
37% ANF, 23% CHG, 8% EHG, 23% WHG, 6% SWA

Lets look at Syrian now
15% ANF, 30% CHG; 0% EHG, 4% WHG, 35% SWA

isn't it obvious that the Levant cannot be the source for the post-Neolithic shift in southern Europe (however we call it) ? The population which moved through the Mediterranean was far more CHG - heavy, with only minor SWA component.
instead, the source looks like it was some early Bronze Age groups which probably no longer exists in western Asia, due to Afro-Asiatic (Semitic) expansions. Hypothesizing here, but it was probably something like Armenians, before they got Arab-shifted in the Iron Age.

"E-V13 existed in Neolithic Europe but was very rare. E-V13 in modern Southern Europe is not of mostly EEF origin"

The first part is true, but the second speculative
E -V13 doesn't exist (virtually) outside the Balkans. So it cannot have come from any recent group. It's probably an in situ founder effect in the Balkans, at some yet to be determined point.

Ariele Iacopo Maggi said...

"E -V13 doesn't exist (virtually) outside the Balkans."

http://www.eupedia.com/images/content/Haplogroup-E-V13.gif

Rob said...

Sorry, that should have said Europe

Matt said...

In the exercises modeling poplations with outgroup D-stats (with nMonte, etc), the Sardinian population looked to me like a mix of around 50:50 Early Neolithic:Recent Italians.

Given a choice of 4 Italian populations (Tuscan, Bergamo, East Sicilian, West Sicilian), Early Neolithic Cardial (Iberian_EN, Anatolia_Neolithic), WHG, Palestinian and Druze, Sardinain nMonte'd as 48.3% Italian (mainly Tuscan and East Sicilian), 49.5% EN (38.7% Iberia_EN, 10.7% Anatolia), 2% WHG, with no Druze or Palestinian.

Depends on what the recent Italians are descended from, exactly, but that seems like the model for recent Sardinians that fits OK with the history for me. More or less Early Neolithic up through the Bronze-Iron Age, then quite heavily settled by Roman-era Italians (and possible Spanish).

In the Eurogenes K15, the Sardinian population described as

Sardinian
West Med 48.22
Atlantic 21.19
East Med 17.48
North Sea 5.54
Baltic 3.23
Red Sea 2.56
West Asian 1.01
Oceanian 0.32
Northeast African 0.2
Eastern Euro 0.15
Sub Saharan 0.05
Siberian 0.03

Rob said...

Thanks for your insights Matt
That settles things
Now - as to Bronze Age Italians ..... ;)

truth said...

Haplogroup J2 is related with CHG, not SW-Asian. There is ancient samples who are J2 and barely have any SW-Asian, but lots of CHG.

Karl_K said...

@Ariele

"No way!!!
Sardinians on k15 are almost identical to anatolian farmers with some less east med and red sea and more baltic and north sea (but it was alredy present in Oezti)... Nope, Sardinians are very close to be 100% EEF. 50% modern italian!!! And modern italian are 50% of what? Nonsense!!!"

Of course, I couldn't agree more. In my own personal estimation, however, modern Sardinians are actually 128% EEF. It seems that the excess 28% was diluted out when traveling back in time.

Ariele Iacopo Maggi said...

Karl_K Matt

You two are hysterically funny!

Ne6, Sardinian, Oetzi

North Sea: 0 / 5,54 / 6,21
Atlantic: 22.5 / 21.19 / 25,54
Baltic: 0 / 3,23 / 0
West Med: 52,55 / 48,22 / 47,53
West Asia: 0 / 1.01 (Finland and basque are the only european that score lower then that) / 0
East Med: 20,16 / 17,48 / 20.11
Red Sea: 4,78 / 2,56, / 0,6

Yes, they have some 3% more Baltic! Maybe some extra WHG that they found on their way to Sardinia... I'll give you that, they are only 97% EEF.

Nirjhar007 said...

If any bud is interested
http://www.nature.com/ejhg/journal/vaop/ncurrent/full/ejhg201660a.html

Kurd Dgk said...

According to my Eurasia K10 (Gedrosia DNA) calculator at Gedmatch:

Population Sardinian Stuttgart Iceman
CHG 10.39 6.59 0
Amerindian 0.02 0 0
W_African 0.15 0 0
Papuan 0.12 0 0
SW_Asian 11.73 13.16 0
S_Indian 0.05 0 0
E_Asian 0.03 0 0
WHG 32.77 22.24 30.35
Anatolian_Farmers 44.68 58 69.64
EHG 0.06 0 0

capra internetensis said...

@Nirjhar

Thanks!

Matt said...

@ Ariele, well perhaps for your next trick use Loschbour's K15 scores to explain to us how much ancestry Northern Europe has from WHG. ;)
To reiterate, Sardinians are mostly EN, in my view, probably because Italians are mostly EN and because Sardinians also have a large (50%) contribution of direct ancestry from the EN. The components for Eurogenes I included only in the view of the lack of any SW_Asian / Red_Sea type component.

@ Nirjhar, that's a quality contribution! Thanks. Shame I can't look at it (not even SI). I'm particularly interested if there are any divergences in the mainland East Asian populations from the existing datasets we have.
Datasets on this on EGA - https://ega-archive.org/studies/EGAS00001001738 Not sure if this is open access, does not look like it.

Shaikorth said...

@Matt supplements here.

http://www.nature.com/ejhg/journal/vaop/ncurrent/suppinfo/ejhg201660s1.html

Matt said...

Thanks Shaikorth.

I'm mainly interested in the Burmese population, so nice to see that it recapitulates what was found by the Harappa on the Burmanese (and other projects) with Treemix showing an admixture edge to a Sino-Tibetan population from what looks more like an ASI root (25%-33%).

In their ADMIXTURE, it seems that there is a low level presence of the Austronesian modal component in most mainland East Asians (not Burmese, some Han Chinese, and some minorities from China), and even Japan. Whether that represents something literal or a signal of particular drift is unclear.

Also, am I understanding the Table S5 correctly, that is suggests particularly shared signals of selection between CHB, Vietnamese and Burmese? (Despite 25% ASI in the latter by f4 models).

The FST values in Table S1 seem kind of odd to me as well, though, as it seems like there's relatively low FST between Bajo-Burmese, despite no real link in the ADMIXTURE and Treemix where Bajo are Austronesian+Papuan, along with strangely no decrease in FST for Burmese-South Indian, even though Burmese is South Indian admixed.

Shaikorth said...

Looking at their TreeMix run, the actual South Indian sample used here is not too different from the North Indian one. Burmese get their migration edge from something that is likely much closer to ASI. Drift should affect fst-stats. Would be great if the researchers started including Est for comparison...

Subcontinental influence aside, Chinese, Burmese and Vietnamese form a distinct unit in the tree, and might have been subject to same selective pressures at some point.

Nirjhar007 said...

Matt , Shaikorth, Capra

Are you able to access the full paper?.

capra internetensis said...

@Nirjhar

Not me, only the supp info.

Nirjhar007 said...

Throw me your mail . You can in my blog , I will not publish it :) .

Matt said...

Shaikorth, sorry for the late reply, yes in the treemix, the edge to the Burmese is more basal to the East Eurasian clade than the South Indian population. However, in the admixture, some existence of North Indian components in Burmese seems more consistent with ancestors like Hakkapikki than the most ASI dark green Paniya (probably somewhat similar people to present day Bengalis). I wonder if there is some compositing in the treemix of related ancestry between India and SE Asia. Although also some *very* minor components linking to Oceanians were present.

FST differences should be affected by drift, but in systematic fashion (if FST increases drift, should be from all populations). EST score would be interesting.

Subcontinental influence aside, Chinese, Burmese and Vietnamese form a distinct unit in the tree, and might have been subject to same selective pressures at some point.

Yes, that could even be admixture after, if the shared ancestral unit (population) carried some distinctive cultural practices or subsistence methods with them that persisted after admixture with other populations.
One thing they did find interesting was that the Burmese became more of an an outlier, reducing clustering shared, once a different measure than iHs was used XP-EHH, with the Han was used as an outgroup.

Also, if anyone wants to read the full paper, this is on researchgate.net:

https://www.researchgate.net/publication/304004026_Multi-layered_population_structure_in_Island_Southeast_Asians

Nirjhar, thanks for the offer though btw.

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Mc Michael said...

Not quite convinced that the ancient Iranians and modern Indians/Pakistanis were identical. The latter surely has stronger affinities to south Asian ghost populations, yet to be uncovered (ie. Dravidians). Also, it's unfortunate, this study lack samples from Eastern Turkey, too, which I'm certain be on a cline starting from the Western Anatolian Neolithic samples all the way to Neolithic Zagros Iranians. Without more populations as a reference, most PCAs will paint a misleading picture. Admixture analysis, at K=13 reveals strong differences between Neolithic Iranians and South Asians, instead Neolithic Iranians showing more similarity with Caucaus Hunter Gatherers. And just look at Global PCAs with modern Iranians and Turks - they practically overlap. That suggests there would have been almost a complete population displacement in Iran! Alternatively, it may be that most populations of Neolithic Iranians from the Zagros region, were less differentiated from paleolithic populations which became ancestral to Indians, than Neolithic Iranians which emerged from other areas of the plateau, and became dominant.

Davidski said...

No one ever claimed that ancient Iranians and South Asians were identical. But South Asians do carry high ratios of Neolithic ancestry from Iran.

Also, Neolithic farmers and a Hunter-Gatherer from different sites in the Zagros and from the South Caspian are all very similar, but very different from modern-day Iranians.

So clearly what seems to have happened is that after the migration of Neolithic farmers from Iran to South Asia, a variety of populations from west of Iran moved into Iran after the Neolithic, replacing and absorbing the descendants of Neolithic farmers in Iran.

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