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Friday, June 3, 2016

Neolithic genome from Iran SMBE 2016 teaser


Update 18/06/2016: Genetics of an early Neolithic pastoralist from western Iran (Gallego Llorente et al. preprint)

...

The paper is probably coming very soon. This is an abstract of an SMBE 2016 talk to be held in four weeks (emphasis is mine):

The shift from hunter-gathering to food production, the so-called Neolithic Revolution, profoundly changed human societies. Whilst much is known about the mode of spread of people and domesticates into Europe during the Neolithic period, the origin of this cultural package in the Ancient Near East and Anatolia is poorly understood. By sequencing the whole genome (1.39x) of an early Neolithic woman from Ganj Dareh, in the Zagros Mountains of Iran, we show that the eastern part of the Ancient Near East was inhabited by a population genetically most similar to hunter-gatherers from the Caucasus but distinct from the Neolithic Anatolian people who later brought food production into Europe. Despite their key role in developing the Neolithic package, the inhabitants of Ganj Dareh made little direct genetic contribution to modern European populations, suggesting they were somewhat isolated from other populations in this region. Their high frequency of short runs of homozygosity, comparable to other early Neolithic farmers, suggests that they overwintered the Last Glacial Maximum in a climatically favourable area, where they may have received a genetic contribution from a population basal to modern Eurasians. Thus, the Neolithic package was developed by at least two genetically-distinct groups which coexisted next to each other, implying a degree of cultural yet little genetic exchange among them.

Gallego Llorente et al., The Neolithic Revolution developed among geographically adjacent but genetically distinct populations, oral presentation (35146), Society for Molecular Biology and Evolution Conference 2016

See also...

Another ancient genome from Iran coming soon

On crop dispersal in prehistoric Central Asia

111 comments:

Davidski said...

A couple of SMBE 2016 abstracts about East Asia...

The Neolithic in Northeast Asia in light of a 7,700 year-old genome (34323)

Veronika Siska 1 , Eppie Ruth Jones 1 , Tatiana Balueva 2 , Jong Bhak 3 , Daniel G. Bradley 4 , Yunsung Cho 5 , Anders Eriksson 1 , Marcos Gallego Llorente 1 , Michi Hofreiter 6 , Sungwon Jeon 3 , Hakmin Kim 3 , Hyunho Kim 5 , Kyusang Lee 3 , Ron Pinhasi 7 , Elizaveta Veselovskaya 2 , Andrea Manica 1

Ancient genomes have revolutionised our understanding of Holocene prehistory in Western Eurasia, but Asia has received limited attention. Here we report genomic data from two individuals from an early Neolithic site, Devil’s Gate (7742-7638 cal years before present) in East Asia, on the border between Russia and Korea. These hunter-gatherers are genetically most similar to geographically close populations from the Amur Basin, in particular the Ulchi, implying a high level of continuity in this region over most of the Holocene. Japanese and Koreans, who live further south, also showed genetic affinity to Devil’s Gate; both these modern day populations were best described as mixes of a population close to Devil’s Gate, likely the ancestral hunter-gatherers who inhabited that region, and modern populations from southern China and South-East Asia, possibly linked to the onset of the Neolithic around 8,000 years ago in the region. Thus, in contrast to Western Eurasia, East Asia experienced a higher degree of continuity, with little input in the northern regions and an integrations of incoming farmers and local hunter-gatherers further south.

Davidski said...

The preliminary report for the deep sequencing of the prehistoric Jomon genome from the Japanese archipelago (35341)

Hiroki OOTA 1 , Takashi Gakuhari 1 , Hiroki Shibata 2 , Tadashi Imanishi 3 , Ryan Schmidt 1 , Martin Sikora 4 , Thorfinn S Korneliussen 4 , Hiromi Matsumae 1 , Takehiro Sato 5 , Takafumi Katsumura 1 , Kae Koganebuchi 1 , Takayuki Nishimura 6 , Shigeki Nakagome 7 , Shuhei Mano 8 , Ryosuke Kimura 9 , Kentaro Shimizu 10 , Atsushi Tajima 5 , Shoji Kawamura 11 , Shigekazu Higuchi 2 , Akira Yasukouchi 2 , Tetsuaki Wakebe 6 , Toshiyuki Tsurumoto 6 , Motoyuki Ogawa 1 , Tsunehiko Hanihara 1 , Hajime Ishida 9 , Yasuhiro Yamada 12 , Hiroimi Shitara 13 , Nobuo Shigehara 14 , Eske Willerslev 4

After the late-Paleolithic period in the Japanese archipelago, the Jomon culture starts around 15,000 years ago, and the Yayoi culture took place of it around 3,000 years ago. The former is a culture by the indigenous people who have hunting-gathering life style, whereas the latter is a culture of large-scale rice cultivation that would be brought by immigrants (and their descendants) from the East Asian continent. Many of previous studies based on skeletal remains have described that the Jomon people have been morphologically homogeneous for more than 10,000 years. The dual structure model for peopling history of modern Japanese has been proposed; according to the model, the Jomon and the immigrants have gradually admixed since the Yayoi period, and the modern main-island Japanese have been formed at last. Our recent study based on computer simulation using genome-wide SNP data from modern Chinese and Hokkaido Ainu, however, has estimated that the admixture between the Jomon and the immigrants occurred 5~6,000 years ago that is twice older than the estimates based on the archaeological evidences, suggesting a possibility of gene flow from the East Asian continent before the Yayoi culture starts.

To resolve the discrepancy, we organized a research team of the Jomon genome sequencing, including physical anthropologists, physiological anthropologists, archaeologists, and researchers of statistics, genomics, and population genetics. We conducted prescreening for the Jomon specimens excavated from various sites by using the next generation sequencer (NGS). The states of preservation of DNAs from the specimens in the Japanese archipelago were commonly even worse than those in Europe and America, because of acid soils, and warm and high humid climate. But, a couple of specimens showed more than 1.0% mapping ratio. Here we present the results of preliminary analyses, and discuss about feasibility of the deep sequencing of Jomon.

Seinundzeit said...

I wonder if the idea Matt and me had will be verified, mainly that perhaps South Asian/South Central Asian/Iranian plateau CHG-like ancestry has much less of an affinity to Villabruna than Satsurblia/Kotias.

I think it might turn out to be correct, considering that "the inhabitants of Ganj Dareh made little direct genetic contribution to modern European populations...".

Rob said...

HHmm

The boldened part "Despite their key role in developing the Neolithic package, the inhabitants of Ganj Dareh made little direct genetic contribution to modern European populations, "


Appears to suggest that the source of CHG in Yanaya wasn't 'Central Asian' admixture , but something closer to EE itself ?

My bet would be that CHG was already lurking around Crimea, the Caucasus, and lower Don by 5000 BC

Rob said...

Is this the Conf @ GC ?

Samuel Andrews said...

Interesting. Don't think we'll see Y DNA R1 but maybe.

@Davidski,

Does CHG peaking at 50% in Georgians make sense to you? Do you think there's also significant CHG ancestry in Northern West Asians; Iran, Iraq, Turkey.

Davidski said...

These Iranian samples will be J, and maybe H and L. Can't see them having any R, unless it's some wayward branch related to R2 or R1b-V88.

Georgians at ~50% CHG sounds about right. But it depends on how you define CHG, because modern Georgians, unlike Europeans, probably have some of this early Neolithic CHG-like component from Iran.

Davidski said...

Yeah, SMBE 2016 is at the Gold Coast. I'm gonna try and get there for this talk. Can't promise that I will though.

Nirjhar007 said...

Let be serious here. One sample? and that of a female. They are not also the cave samples , supposed to be the ancestral genome of European R1a .

Rob said...

Yes we'd all love to see more samples.
Hopefully this'll be one of many to come.

Davidski said...

They are not also the cave samples, supposed to be the ancestral genome of European R1a.

So the fact that they were buried in a cave means they're different from the nearby Zagros farmers?

And supposed to be R1a according to who?

Nirjhar007 said...

They are 1000 KM apart from each other bud . Me...

Nirjhar007 said...

and Even without Y-DNA from Ganj dareh area , its not good approach in any standards. I actually can't believe they are publishing a single sample , of a female.....

Davidski said...

Apparently the south Caspian region was an Ice Age refuge.

So where do you think the ancestors of these CHG-like but distinct Zagros farmers spent the Ice Age?

Karl_K said...

"Despite their key role in developing the Neolithic package, the inhabitants of Ganj Dareh made little direct genetic contribution to modern European populations, suggesting they were somewhat isolated from other populations in this region."

That's fine, but what about a contribution to other modern populations outside of Europe?

These teasers... really tease.

Karl_K said...

"and Even without Y-DNA from Ganj dareh area , its not good approach in any standards. I actually can't believe they are publishing a single sample , of a female....."

Wow! You have pretty high standards! I guess they should have just chucked this one in the bin. Why are they wasting everyone's time with new data?

Nirjhar007 said...

So where do you think the ancestors of these CHG-like but distinct Zagros farmers spent the Ice Age?

For the moment , we need those N Iranian cave samples first. I have mailed Pinhasi ...

Nirjhar007 said...

For new data Karl, we need also Y-DNA and numbers ...

Karl_K said...

Well hold on Nirjhar007,

Firstly, for new data we should wait for an actual publication instead of a meeting abstract.

Secondly, although Y-DNA is definitely interesting and informative, it is much much much less informative than a 1.39x whole genome sequence, even from a single individual.

epoch2013 said...

European EF look like Sardinians and not Middle-Easterners. That is explained by additional gene flow/migrations in the Middle-East after the neoloithic expansion into Europe. Could this be one of the sources for that?

Stranger is the fact that it is related to CGH but did not contribute to Europeans. If Yamnaya is half CHG, and northern Europe has more than 50% Yamnaya, how can that be? Anatolia_EN is clearly the source of European EN. But what is the source for Yamnaya's non-EHG part?

This one is going to be very nice playing around with.

Davidski said...

But what is the source for Yamnaya's non-EHG part?

It's definitely CHG. Not CHG-like, but CHG from the Caucasus.

Samuel Andrews said...

@Karl_K,
"That's fine, but what about a contribution to other modern populations outside of Europe?

These teasers... really tease."

Europe is huge and farming expanded there relatively quickly. It's a significant event in in prehistory. What they're doing in this abstract is crossing out the possibility Iranian farmers brought the practice to Europe and confirming that Turkish farmers were the ones who did that.

capra internetensis said...

CHG-like in the east - not a surprise. Will be very interesting to see how this relates to the Indian Neolithic and the post-EEF ancestry of the Middle East.

@Nirjhar

Wow, dude. Y DNA is one locus. A very interesting locus, but small potatoes compared to a full genome. We have a Neolithic Eastern Fertile Crescent sample and you are whining because it's a *girl*? Yeesh.

epoch2013 said...

@David

It's definitely CHG. Not CHG-like, but CHG from the Caucasus.

It probably is wiser to wait until the results are published. However, their clear statement that these didn't contribute to Europeans looks hard to reconcile with Yamnaya's half CHG. Unless Zargos is a type of its own, merely closer to CHG than Anatolia_EN, but still with considerable distance to both.

There seems to be a lot of substructure in EEF/ENF.

rozenfag said...

@epoch2013 : My reading is somewhat different. If you read carefully, it says:

Despite their key role in developing the Neolithic package, the inhabitants of Ganj Dareh made little *direct* genetic contribution to modern European populations, suggesting they were somewhat isolated from other populations in this region.

So they could've made indirect contribution, through Yamnaya, for example.

Davidski said...

However, their clear statement that these didn't contribute to Europeans looks hard to reconcile with Yamnaya's half CHG.

I fail to understand your line of reasoning.

Yamnaya has ancestry from CHG in the Caucasus, not this CHG-like population from Iran.

Davidski said...

So they could've made indirect contribution, through Yamnaya, for example.

Doubt it. They would've said something if this genome rejected their earlier finding that Yamnaya was half CHG.

Simply, Yamnaya is half CHG, and this Iranian Neolithic group is CHG-like, but easy to tell from CHG.

I have a feeling that epoch is on a fishing expedition for something that he had an eye on but didn't work out.

epoch2013 said...

@Rozenfag

So, CHG-like as in comparison to Anatolia_EN?

@David

I think Rozenfag already addressed it. I read into the line that it was part of a CHG population. That population has been known to add to Yamnaya.

Davidski said...

I read into the line that it was part of a CHG population. That population has been known to add to Yamnaya.

No it wasn't. They say...

- genetically most similar to hunter-gatherers from the Caucasus

- somewhat isolated from other populations in this region

It wasn't CHG and didn't contribute to Yamnaya. What is your problem exactly?

Alberto said...

While we probably already expected that the Zagros EN would be CHG-like it's great to have it confirmed and hopefully soon to have the genome available.

Abstracts can be misleading to try to get fine details. Kotias and Satsurblia by formal stats also didn't show to have made a great contribution to modern Europeans (at least compared to Anatolia_Neolithic), so maybe this genome will behave similarly. Let's wait and see.

But didn't Kotias/Satsurblia show signs of having gone through a population bottleneck during the LGM or something? Apparently this one doesn't, so probably a better reference for Asia at least.

Davidski said...

Alberto,

Kotias and Satsurblia by formal stats also didn't show to have made a great contribution to modern Europeans (at least compared to Anatolia_Neolithic), so maybe this genome will behave similarly. Let's wait and see.

I'm glad you added "at least compared to Anatolia_Neolithic", otherwise your comment wouldn't make any sense.

But I very much doubt this Zagros population will be comparable to CHG in the influence it had on Europe.

Iran doesn't look like the source of anything but minor admixture in Europe.

Nirjhar007 said...

Just one sample , irrespective to its coverage value . Is not enough, I am sorry . There is always the great danger of randomness , to establish the pattern, which can scientifically indicate to something . We need more.

Capra,

SNP's are very important . Mtdna is less important and indicative than Y-DNA . That is certain....
D,

But I very much doubt this Zagros population will be comparable to CHG in the influence it had on Europe.

Just cling on to it....

Davidski said...

Cling onto reality? Yes, indeed I will.

But all of your kooky theories are crashing down around your ears. You might want to update them soon to something more in tune with reality.

Nirjhar007 said...

Bullshit ...

Davidski said...

No bullshit mate.

Your Out of Iran PIE theory and Out of India Indo-Iranian theory are just comedy classics.

Nirjhar007 said...

South of Caspian and SC Asia you mean . Well, let the samples come...

Alberto said...

@Davidski

Yes, I think you understood correctly what I meant. The "little contribution" might be relative to Anatolia_Neolithic, and it might be based on formal stats, not ADMIXTURE. So this would be consistent with what we see with Kotias. I just wouldn't read too much into cryptic sentences in abstracts. When we see the paper we'll know what it really means.

And what's happening with all the ancient DNA related to the LN/BA transition? We're already more than 6 months of drought. The previous year and a half there were always teasers, conferences, new papers... And suddenly everyone went silent about it. Something big must be on the works, but I wonder why they no longer give hints about it, no talks, nothing.

Davidski said...

Apparently the Broad MIT/Harvard and Copenhagen teams are working on a Indo-European paper, with new samples from the steppe, Central Asia and South Asia.

It's pretty much now a foregone conclusion though, that the Proto-Indo-Europeans came from the steppe, and that their spread was aided by the plague. That's why there aren't any new updates. They don't have anything new to say.

You should ask Nirjhar about the new samples...they include BMAC, Swat and Harappa.

Karl_K said...

"Just one sample , irrespective to its coverage value . Is not enough, I am sorry . There is always the great danger of randomness"

I guess this is true. I mean... just imagine if we only had one EEF (pick any of them as the example) and one WHG (again pick any of them) and only one Yamnaya, etc.

Actually... that great danger of randomness doesn't seem like such a great danger. Most of the ancient DNA samples largely cluster with others of the same group based on archaeology, location, and date.

Maybe a few surprises of randomness, but not very many.

It is very reasonable to assume that this genome will be similar to most of the others in the same region around the same time (until proven otherwise).

Alberto said...

That sounds great. I hope it won't take too long.

They didn't say anything about Asia, so I think they should have something new to say about it. With the Samara samples we were hearing about them for 6 months or more before publication. I find it strange (and at this point slightly annoying) that they now completely stopped giving any information about what they're working on.

People are irritable here lately. The new information at least would calm things down. Good that Nirjhar wrote to Ron Pinhasi to complain. If I had his contacts I would do the same.

Rob said...

Davidski

"that their spread was aided by the plague"

Isn't the earliest date from 2500!Bc ?
That's a little too late for everything

Davidski said...

Pinhasi won't save Nirjhar's theories.

You think the Belt/Hotu Caves samples haven't had their Y-chromosomes scanned yet? Think again.

Grey said...

"Simply, Yamnaya is half CHG, and this Iranian Neolithic group is CHG-like, but easy to tell from CHG."


If the Caucasus CHG mixture in PIE were farmers at the time they moved onto the steppe (?) and yet distinguishable from these isolated Taurus CHG-like farmers and the Anatolian farmers does that imply three separate farming centers?

Davidski said...

No, because CT was in close contact with Yamnaya.

Gioiello said...

@ Samuel Andrews

"and confirming that Turkish farmers were the ones who did that".

Those Anatolians hadn't anything "Turkish", as Turks arrived there only a few centuries ago and also now Asia Minor has very low percentage of "Turkish".
All to demonstrate that Europeans derived from Anatolians and not that the other way around happened.

Rob said...

That doesn't follow
The earliest plague gene on the steppe is from 25-2000 BC. That's even after Yamnaya , and 1500 years after the Balkan collapse
There's a lot more to it, trust me

But look one has to say: this abstract, with all deserved caution, doesn't look too good for an out of central Asia hypothesis. But obviously we need this sample data, and more

Davidski said...

Both Afanasievo and Corded Ware had it, so duh, who did it spread with?

Rob said...

Dave

The issue isn't that CWC Samples have yielded pathogens. But have we concluded how virulent they were and the incidence of carriers ? For an epidemic to occur, we need a threshold carrier incidence, and nativity in the newly recipient populations. Given that the rest of Europe already had exposure to animals, and in fact were the source for steppe domesticates, we are posed with a conundrum. At present still idea is interesting but hypothetical, but ultimately too late chronoligically

So the main issue you're ignoring is that the Neolithic collapse ante dated these CWC carriers by 1500 years.
Did the fleas teleport back in time to France or uk ?

Davidski said...

What I said was that both Afanasievo and Corded Ware had the virus, so their common ancestors also had it.

It's common sense, and that's the general idea accepted now among the scientists studying the phenomenon.

Btw, the Afanasievo samples with the virus are contemporaneous with Yamnaya. So there's also that.

Rob said...

Interesting rationalisation
So Mal'a boy must also have had it
Btw it's not a virus, but a bacterium. Might want to brush up on your microbiology
And your maths whilst your at it (4200 BC comes before 3000 BC)

Davidski said...

The earliest sample with Y. pestis is Afanasievo RISE511 dated to 2909–2679 BC. That's contemporaneous with Yamnaya is it not?

Nirjhar007 said...

You think the Belt/Hotu Caves samples haven't had their Y-chromosomes scanned yet? Think again.

That has nothing to do with the study .

And for arguments sake, if this sample was male and of R1a/R1b , then there would have been turmoil here .

We do know that, there is no exclusive relation between SNP's and Autosomes..

Davidski said...

You know what, there might be a conspiracy against the awesome South Caspian PIE theory. Because being so awesome it's difficult to understand why it hasn't come out on top yet...or even been taken seriously.

VOX said...

What about the Mesolithic/Palaeolithic people of Iran? Are they expected to be CHG or something completely different? Also what about modern Iranians? Since they are not pure CHG, what demographic expansions in the past lead to them being more EFF/Anatolia admixed.

Davidski said...

Mesolithic Iranians will be like early Neolithic Iranians, because local hunter-gatherers in the Zagros developed farming and herding. So they'll be CHG-like, but not CHG, and probably more basal.

Iran has had a very complex genetic history. It'll take years to get on top of it all with ancient DNA.

Nirjhar007 said...

Also , they didn't speak about the relation with the Asians . They Indicate its an Isolated one .


CHG surely existed In Iran , and S Asia got ''actual'' migrations from Iran , from Neolithic times.

Iranocentrist said...

Hi Mr David, do you think this will be a high coverage sample? And, would you be able to do a global PCA based on it once it is released?

postneo said...

It is to be expected that yamnaya would be more caucasus like than Zagros because caucasus is closer.
It would be good to know the closest living descendants of this sample.

It would be fabulous if Reich, Pinhasi et al. were able to test all ancient samples for plague and other pathogens. Is it part of the agenda or too ambitious? It took a good 6 months between initial results before yamnaya was tested for such pathogens. Perhaps that loop can be shortened.

Understandable if researchers would like to milk multiple publications out of data.

David's plague theory needs to be tested by establishing a chronological flow from the steppes to other regions. which means testing non steppe samples for plague at the very least !

the earliest virulent plague is from iron age Armenia.

Davidski said...

There's no indication in the abstract that this genome is not typical of the Zagros Neolithic population.

Also, this is where South Asia should have got most of its West Eurasian admix during the Neolithic. So since this genome is CHG-like, then that makes perfect sense.

Of course, South Asia also received CHG proper admixture via the steppe during the Bronze Age. So it's not surprising that South Asians today are so CHG-like.

Davidski said...

Hi Mr David, do you think this will be a high coverage sample? And, would you be able to do a global PCA based on it once it is released?

It's 1.39x, which is plenty high enough for a global PCA, West Eurasian PCA and West Asian PCA, and all sorts of other stuff.

Nirjhar007 said...

South Asians today are so CHG-like.
Yes, but there was no migration from steppes that create such impact . Also you months ago sheltered on ''Elite Invasion'' idea .

It was Iran ...

Davidski said...

Yes, but there was no migration from steppes that create such impact.

Very funny.

Red arrow here shows it...

https://drive.google.com/file/d/0B9o3EYTdM8lQTldVNWlZQm0xVzA/view?usp=sharing

Nirjhar007 said...

No there wasn't mate, stop playing with common ancestry . That's why they mutate to ''BMAC mix'' invasion, which is not funny but killer funny...

postneo said...

"There's no indication in the abstract that this genome is not typical of the Zagros Neolithic population."

How would the researchers know what is "typical of zagros neolithic" when they only have this one sample? you mean modern zagros perhaps. They abstract seems obsessed with contribution to far away Europe and not a word about local continuity/discontinuity. I think thats the norm.

VOX said...

Hi Davidski,

Thanks for your explanation. I'm guessing that Y chromosomes L, J2 and possibly R2 might be a legacy of CHG.

BTW since you do a lot of data manipulation/visualization, here is a tool that you might be interested in.

http://julialang.org/

It's syntaxed similar to python but runs nearly as fast as C with built in arrays and an elegant data-frame library.

Play with it here: http://www.tutorialspoint.com/execute_julia_online.php

postneo said...

"https://drive.google.com/file/d/0B9o3EYTdM8lQTldVNWlZQm0xVzA/view?usp=sharing"

David you are fooling yourself. you don't need software to draw such an arrow. Andronovo is older than modern south asian and the geographically nearest ancient sample to south asia. So any right minded software or human would draw such an arrow.

Davidski said...

@postneo

Andronovo is older than modern south asian and the geographically nearest ancient sample to south asia. So any right minded software or human would draw such an arrow.

O really?

Except the software wasn't fed geographic coordinates or even Y-HG data, and the Andronovo and Srubnaya samples are practically like modern Northeast Europeans in terms of genome-wide structure, which is what the tree is based on.

So how about you actually come up with a coherent argument for once?

Iranocentrist said...

@Davidski
"Red arrow here shows it...

https://drive.google.com/file/d/0B9o3EYTdM8lQTldVNWlZQm0xVzA/view?usp=sharing"

Pardon my ignorance of the finer details of Treemix and I might be completely wrong, but the red arrow starts from the branch that is ancestral to the steppe groups and not of the steppe groups, so could this be also interpreted that there yet remains an unsampled group that could be ancestral to both the Steppe z93 and Indian Z93?

Davidski said...

The admixture edge is a sister clade to the steppe groups, so the European population that migrated to India had the same structure as the steppe groups.

And we already know the genetic structure of the steppe groups; EHG, CHG, plus EEF from the Middle Bronze Age. R1a, including Z93, comes from the EHG part.

They're not a mystery. The only mystery left is the genetic structure of South Asian hunter-gatherers.

Iranocentrist said...

But doesn't the Steppe theory explicitly state that it was Andronovo/Sintashta which Invaded India and Iran?

Davidski said...

Yes, it was an Andronovo group, but probably not the Andronovo group we have sampled at the moment.

postneo said...

"Andronovo is older than modern south asian and the geographically nearest ancient sample to south asia. So any right minded software or human would draw such an arrow.

O really?

Except the software wasn't fed geographic coordinates or even Y-HG data, and the Andronovo and Srubnaya samples are practically like modern Northeast Europeans in terms of genome-wide structure, which is what the tree is based on."


The software is picking the nearest ancient sample in time and space and given the meager choices Its the best approximation of a BA ancestral population. If there was a Baluchi/Afghan/Uzbeg/indian BA sample I am sure any of them would win over andronovo in treemix

Rami said...

David you don't know basic math.
The populations in S.SC Asia would have already been very CHG rich LONG before the arrival of steppe nomads. The steppe nomads do not have any where near the levels of CHG , those populations did. If anything they would have reduced the amount of CHG in SC Asians not increased it, because they would have brought WHG to that part of the world.

batman said...

@ Davidski

"Apparently the south Caspian region was an Ice Age refuge."

Interesting.

Is there any archaological repports existing, producing a timeline of evidence throughout the Late Paleolithic, nessecary to explain this 'apparent' apearance?

Seinundzeit said...

Andronovo was, for all intents and purposes, quite similar to modern northern European populations, like Lithuanians (albeit with much less EEF/WHG affinity and much more CHG/EHG affinity than any modern northern European population).

So if these migration edges are just reflective of a native Bronze Age South Central Asian population, then that native Bronze Age South Central Asian population would have to be identical to Andronovo. So, it seems the claim here by some is that BMAC/IVC were almost identical to Andronovo, and very similar to modern Northern Europeans. But that makes no sense. Anyone making such an argument is engaging in a classic example of special pleading

But one can play along, and test scenarios. David has already done so. If one assumes heavy MA1-related ancestry in South Central Asia, prior to any Indo-Iranian influx, we have this graph:

https://drive.google.com/file/d/0B9o3EYTdM8lQRTI5QU1NY05kV2M/view?usp=sharing

A relationship between MA1 and South Asia is verified, but the upper caste North Indian samples still turn out to be almost 50% LN/EBA European. So, that's not a feasible argument.

Now, if we assume that South Central Asians/South Asians have significant amounts of CHG-like ancestry, we can see if the LN/EBA European migration edge still happens when we include Satsurblia/Kotias. An example:

https://drive.google.com/file/d/0B9o3EYTdM8lQOU9BcG92R2ZiOFU/view?usp=sharing

CHG is on the graph, yet (again) the upper caste North Indian samples are still around 50% LN/EBA European.

Basically, as David has noted, countless topologies in TreeMix replicate a massive migration edge from EBA steppe populations into upper caste northern South Asians (and a slightly lesser one, but still very substantial, into South Indian Brahmins). It's a basic finding, happens all the time.

Regardless, it's pretty simple. South Central Asians like the Pamiri Tajiks are anywhere from 40%-70% genetically derived from the cluster of Sintashta/Andronovo/Srubnaya-related populations, probably around 60%. South Central Asians like the Pashtuns/Kalash/Nuristani/Kohistani are anywhere from 30%-50% genetically derived from the cluster of Sintashta/Andronovo/Srubnaya-related populations, probably around 40%. And upper caste North Indians are anywhere from 30%-50% genetically derived from the cluster of Sintashta/Andronovo/Srubnaya-related populations, probably around 40%. This ties in very well with the uniparental data.

All that remains is figuring out what the non-steppe ancestry of South Central Asians/South Asians really is (a lot of questions here, many complex issues, etc), getting a tighter range of estimates for the steppe ancestry of these populations, and figuring out which population received it's steppe ancestry from which steppe wave (Indo-Aryan, Indo-Scythian, Kushan/Yuezhi, White Hun/Hepthalite, etc). That's really it.

Gill said...

What are the odds you think of finding a Neolithic population from Central Asia that are Hunter Gatherers closely derived from MA1/ANE-like ancestors, but beginning to intersect with Neolithic Farmers from the Southwest?

Right now it seems like the spread of hunter gatherers dictates everything. ANE from Siberia, WHG from northern Europe, EHG in the middle, etc. So there's a gradient of ANE with SW-Asian/ENF-like stuff in CHG. It stands to reason there would be a higher ANE proportion somewhere in Central and South Central Asia (being closer to Siberia). They could even have developed before the Neolithic depending on how far the ancestors of near eastern farmers got before developing farming.

They would be very CHG-like, but not derived from CHG but rather share common ancestors with CHG. The Gedrosian idea fits this very well, especially with the sequencing of MA1, but I think a missing piece of the puzzle is suitable Early Neolithic (or earlier) Near Eastern/Southwest Asian DNA.

So if this Neolithic Iranian DNA can be run though one of the ANE calculators and winds up with 35% or more ANE... I think that confirms it. That also explains South Asia. The Bronze Age European-like populations had high ANE as well, but not as high as, say, Burusho. The only turnover winds up being European hunter gatherer-like admixture for Neolithic Near Eastern farmer-like admixture with the MA1-like stuff staying high. So the reason South Asia has high ANE is because there hasn't been as much migration or population turnover in the past 2000-3000 years compared to the Caucasus and Iran (from the Near East) and Central Asia (from East Asia). South Asians' greater MA1 affinity is kind of are like a snapshot of historic Asia.

Davidski said...

Rami,

Bahaha. Thanks for helping us out with the basic maths.

postneo,

You're talking out of your backside again. I've already taken account of the pre-IA genetic structure in South Asia.

https://drive.google.com/file/d/0B9o3EYTdM8lQTFZpbDFpN1RFaDA/view?usp=sharing

Gill,

It makes no difference if Harappan-era South Central Asians show high levels of ANE in some tests. It's already obvious that there were large scale population turnovers in the region, especially among the upper casts in India.

It's not like genetically similar populations can't replace each other. Although in this case, they're not even all that similar; rather, deceptively similar.

Razib Khan said...

Nirjhar007 makes me want a usenet style killfile.

Jaydeepsinh Rathod said...

Here is something I found which throws some light on the importance of this ancient Iranian Neolithic genome.

http://archaeology.up.nic.in/doc/mn_jfj.pdf

This is a paper on Mehrgarh Neolithic. I am quoting some excerpts from the Conclusion of this paper,

"In spite of some obvious differences, for instance the progressive predominance of the breeding of zebu (Bos indicus), the full setting of farming economy at Mehrgarh displays evident similarities with what had been noticed in the case of the early Neolithic settlements in the hilly regions forming the eastern border of Mesopotamia. The circular houses of the earliest Neolithic villages have not been found at Mehrgarh. But quadrangular houses built with about 60 cm long narrow bricks with a herringbone pattern of impressions of thumbs to provide a keying for the mud-mortar, have been uncovered at several aceramic Neolithic sites in the Zagros, such as Ganj Dareh or Ali Kosh in the Deh Luran region of Iran, where, like at Mehrgarh, traces of red paint have also been noticed on the walls.Circular fire-pits filled with burnt pebbles are also associated to all these early settlements. The lithic industries also show evident parallels, which cannot be developed in this contribution. Nevertheless it can be pointed out that the polished-stone axes begin occurring at several sites of the Deh Luran area, such as Ali Kosh, only in the later phases of the aceramic Neolithic along with an increasing number of stone vessels. It is the same at Mehrgarh where the polished stone axes in black diorite are found only in the upper levels of Period I, mostly as gravegoods."

"No graveyards have been exposed on a large scale like at Mehrgarh, either in the Zagros or Del Luran area, making comparison difficult. But, for instance, the few graves exposed at Ali Kosh show skeletons with positions rather similar to those of Mehrgarh. Among the gravegoods one notices ornaments made of seashells and semi-precious stones such as turquoise, a few beads in copper. Baskets coated with bitumen and oblong-shaped cakes of red-ochre strengthen the parallels. Catherine Jarrige in her contribution has also dealt with the similarities between certain types of figurines. We have also seen the strong parallels between the first occurrence of ceramics built according to the same sequential slab construction and the setting of big multi-cellular granaries at Mehrgarh at the beginning of Period II and at several sites in Mesopotamia, among which Umm Dabaghiyah before and around 6000 BC."

(conti...)

Jaydeepsinh Rathod said...

(...continued)

"The similarities noticed between Neolithic sites from the eastern border of Mesopotamia to the western margins of the Indus valley are highly significant. A sort of cultural continuum between sites sharing a rather similar geographical context marked with an also rather similar pattern of evolution and transformation becomes more and more evident. But the Neolithic of Mehrgarh displays enough original features to imply an earlier local background which has so far not been documented. Nevertheless the cultural dynamism shown by the inhabitants of Mehrgarh as early as level I of Period I indicate that the Neolithic of Balochistan cannot be interpreted as the ""backwater'' of the Neolithic culture of the NearEast."

Summing up, the CHG like genome discovered at Ganj Dareh seems to be of the Gedrosian variety since the Neolithic in Western Iran is very similar to South Asian Neolithic in Mehrgarh which is in Balochistan (aka Gedrosia). Hence the Ganj Dareh genome is in maximum probability going to be very close to the CHG in South Asia which peaks in Balochistan and where the sister site of Iranian Neolithic (i.e. Mehrgarh) exists.

The only complication is that, as expressed in the last few lines, Mehragrh also has elements of South Asian Neolithic, principally the Zebu cattle which also exists in Bhiranna in Haryana since 7500 BC. These specific elements of South Asian Neolithic are not found in Iranian Neolithic sites of Western Iran. Hence, Mehrgarh is probably not a typical Iranian Neolithic site but a combination of South Asian & Iranian Neolithic. So it may also be that the Mehrgarh people are slightly different than people of Iranian Neolithic.

Davidski said...

Forget Admixture components like Gedrosia. We're now way past that sort of stuff.

South Asian Neolithic in all likelihood derives from the Zagros Neolithic, and this Zagros farmer girl genome is probably what the earliest farmers in South Central Asia were like.

Have a look at the maps here...

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0095714

http://hol.sagepub.com/content/early/2016/06/01/0959683616650268.abstract

So it's not very surprising that South Asians have so much CHG-like and CHG-proper ancestry, considering also the Bronze and Iron Age migrations of the Indo-Iranians into South Asia.

Out of India never made any sense. Just deal with it.

Jaydeepsinh Rathod said...

Sein,

"So, it seems the claim here by some is that BMAC/IVC were almost identical to Andronovo, and very similar to modern Northern Europeans. But that makes no sense."

"https://drive.google.com/file/d/0B9o3EYTdM8lQRTI5QU1NY05kV2M/view?usp=sharing

A relationship between MA1 and South Asia is verified, but the upper caste North Indian samples still turn out to be almost 50% LN/EBA European. So, that's not a feasible argument."

Dear friend, I humbly disagree with your interpretation. Correct me if I am wrong but this is how I see the above graph.

We see an arrow coming from the base of branch which has Srubnaya, Yamnaya_Samara, MA1 & Corded_Ware_Germany. This is in addition to an arrow which goes from between the Munda & Indian branch.

What this indicates is this - the arrow into MA1 indicates that there is a shared drift of Indian_North & Indian_South as well as the Munda with MA1 which is absent in Srubnaya, Yamnaya & Corded Ware. This is very old shared drift and has nothing to do with any migration during the Holocene.

On the other hand, the migration edge into Indian North indicates that all the four samples right from MA1 to Corded Ware Germany, share some ancestry with North Indians to the exclusion of Indian South. It does not in any way indicate a North to South migration. If we argue that all South Asian R1a is of recent import from the steppe, it would mean that R1a found among Indian South is also from the steppe. In that case, the migration edge from the steppe related people should not only go into India North but in India South as well.

---------------------

"Now, if we assume that South Central Asians/South Asians have significant amounts of CHG-like ancestry, we can see if the LN/EBA European migration edge still happens when we include Satsurblia/Kotias. An example:

https://drive.google.com/file/d/0B9o3EYTdM8lQOU9BcG92R2ZiOFU/view?usp=sharing

CHG is on the graph, yet (again) the upper caste North Indian samples are still around 50% LN/EBA European."

Here too, the answer seems straight-forward. Indian CHG is not the same as Caucasus CHG - it is of the Gedrosian type. Secondly, the 2nd graph is only indicating the fact that India_North & the steppe-related populations share ancestry to the exclusion of the CHG. And this ancestry is likely through the South Asian - Gedrosian CHG and not the Caucasus one.

Jaydeepsinh Rathod said...

"South Central Asians like the Pamiri Tajiks are anywhere from 40%-70% genetically derived from the cluster of Sintashta/Andronovo/Srubnaya-related populations, probably around 60%. South Central Asians like the Pashtuns/Kalash/Nuristani/Kohistani are anywhere from 30%-50% genetically derived from the cluster of Sintashta/Andronovo/Srubnaya-related populations, probably around 40%. And upper caste North Indians are anywhere from 30%-50% genetically derived from the cluster of Sintashta/Andronovo/Srubnaya-related populations, probably around 40%."

The above, my friend, is not fact but an article of faith. The South Asians & Central Asians were significantly more advanced culturally & more numerous than those steppe populations. Those steppe populations may be argued to have become rulers of Central Asians & then South Asians. But they are unlikely to have eliminated the native culture & native religion. They are more likely to embrace the native culture, language & religion and eventually a few centuries down the line they would completely merge with the local population. Do you see any trace of the Mitanni in Near East today ? Yet you want to argue, that a imagined migration(for which there is no proof) was able to displace the language & religion of the whole of Central Asia & North India, place where equally or more advanced people than those of Near East existed. The Mongols ruled Central Asia for 2 centuries - do you see any trace of their religion or language in Central Asia ? On the contrary a settled agriculture based society is a much more powerful cultural force and if its members were to migrate into a sparsely populated region they're more than likely to preserve & impose their language & culture in the new region.

Davidski said...

@Jaydeepsinh

If we argue that all South Asian R1a is of recent import from the steppe, it would mean that R1a found among Indian South is also from the steppe. In that case, the migration edge from the steppe related people should not only go into India North but in India South as well.

No, because most of the R1a in South India is the result of secondary gene flow from North India, which involved males with minor steppe admixture.

In other words, steppe Y-chromosomes did fairly well in South India, but steppe autosomal admixture was diluted to levels that TreeMix isn't able to pick up.

Jaydeepsinh, did it ever occur to you that I actually know what I'm doing and talking about here?

Shaikorth said...

"What this indicates is this - the arrow into MA1 indicates that there is a shared drift of Indian_North & Indian_South as well as the Munda with MA1 which is absent in Srubnaya, Yamnaya & Corded Ware. This is very old shared drift and has nothing to do with any migration during the Holocene."

Jaydeepsinh, the migration into Ma-1 connects the Munda-Dai-Han branch to ANE, after North and South Indian have split off. While that may indeed be some kind of old drift between Austroasiatics, East Asians and ANE, the migration edge into Indian branch comes from near the steppe populations and is very distinct it.

Kurd Dgk said...

The Gedrosian signal is irrelevant as David has stated, because it appears to be recently differentiated signal from the Caucauses signal which is modal to modern W Asian populations. This is evident from the difficulty in splitting it from Caucauses as well as the small distances between Caucauses and Gedrosian in FST matrices, which is consistent with the migration of proto-Baloch from the NW Iran or Caucauses region within the past 1000 to 2000 years.

The Ganj Dareh sample is much older than this, and it is very unlikely that the mutations at the sites associated with the Gedrosian ADMIXTURE signal allele frequencies had yet started.

Matt said...

Been off my computer for a while, my reactions:

@ Sein

I wonder if the idea Matt and me had will be verified, mainly that perhaps South Asian/South Central Asian/Iranian plateau CHG-like ancestry has much less of an affinity to Villabruna than Satsurblia/Kotias.

Yeah, my view is that they could (especially if they're ancestral to ANI) particularly be lacking in affinity to UHG though basically I see UHG as a side clade to the European Villabruna clade (WHG, more or less) so essentially what you say.

Here's hoping we can test that with some nice D(Mbuti,Anatolia_Neolithic)(CHG,Ganj Dareh), D(Mbuti,Villabruna)(CHG,GD) etc.

Also D(Mbuti,Yamnaya)(GD,CHG), will be interesting. If its inclining to CHG (negative) that's some solid evidence CHG ancestry itself mattered, or if vice versa, for an Iran->Caspian->steppe route for Neolithic ancestry in Yamnaya. Alternatively, if neither are significant, then could indicate another CHG source in Yamnaya, which could be something.

Agree it doesn't seem like they are positioning this (GD) as an ancestry source for Yamnaya, however abstract Kremlinology rarely seems to work out (remembering how excited everyone was that the Kumtepe samples would show something very new - although perhaps they might do better, with the GD reference sample?).

I'm pleased by this abstract, because this is really what we've been wanting as the next step ever since Jones et al with CHG (really ever since Haak et al).

(Longer term, of course we may still need to look at the Kelteminar Culture and see exactly what they were.)

One point I would say is re: direct contribution, since this seems to have good coverage as a sample, they may be indicating that there is not direct contribution by a haplotype analysis, as in Cassidy et al? Haplotype donation, seems a stronger technique for "direct" vs "closely related population" contribution.

Broadly skeptical of the idea of greater paleolithic continuity in Korea than Northern Europe, per the Siska et al abstract. It seems like they may be making some assumptions about what the founder farming populations for the Korean / Japanese Neolithic were like - Southern Chinese like. This may be like assuming Neolithic in Europe as pure basal Eurasian, and thus assuming high continuity, because of course Europeans are closer to the Villabruna cluster than basal). Plus, the possibility of hunter gatherer resurgence may have been stronger in Korea, so the first farming wave may have been different....

Kurti said...

"was inhabited by a population genetically most similar to hunter-gatherers from the Caucasus but distinct from the Neolithic Anatolian people who later brought food production into Europe."

What did I say? The eastern parts of the Near East aka Iranian Plateau will through out people more similar to CHG than Anatolian farmers. Those guys will be probably more Gedrosia shifted though.

Kurti said...

My whole theory from the beginning was, we will deal with two if not three distinct groups. Anatolian_Levant farmers in the West. "Teal like" people on the Iranian Plateau and the Caucasus. I also said those CHG dudes probably came up there from the Iranian Plateau didn't I?

Davidski said...

CHG were native to the Caucasus since the Paleolithic.

This farmer isn't CHG.

And it makes no difference where its shifted in some old Admixture tests.

Point is, there goes the Zagros Indo-European homeland theory. If there ever really was such a theory. Seemed more like an internet hiccup to me.

Kurti said...

take in mind the text also speaks about those Neolithic people from the Iranian Plateau receiving Basal Eurasian ancestry by start of the Neolithic means, before that the Iranian Plateau probably CHG minus the Basal Eurasian portion, which sounds like an ANE like people to me, which makes even more sense, We have a ANE-WHG transition from the Iranian Plateau to Anatolia. ANE mixed with BE on the Iranian Plateau and becomes CHG while in the Levant and Anatolia it mixes with WHG and becomes Anatolia-Levant Farmers.


@Dave I didn't said this farmer was CHG please read properly, I said CHG probably originated from something like this farmer in the Zagros mountains, which was CHG like but more Gedrosia shifted.

Davidski said...

Satsurblia already had Basal Eurasian and that was during the Paleolithic in the western Caucasus.

So Zagros and south Caspian foragers were also part Basal Eurasian during the Paleolithic, and probably during the Ice Age.

Nirjhar007 said...

Razib ,

Nirjhar007 makes me want a usenet style killfile.

That's the effect of politics bud..

Jaydeep,

Wait for the paper to come out. Also the important cave samples .And I do hope, they will publish Y-DNA, from the very Ganj Dareh area.

There is even a possibility that CHG had Indian origins , but I will not say that emphatically now. Lots to see ..

Davidski said...

There is even a possibility that CHG had Indian origins.

Nah, the Y-HG I+J and Villabruna/Satsurblia connections kill that idea.

Maybe Satsurblia has some admixture from near India, but that'll be hard to prove without Ice Age genomes from South Asia.

Chad Rohlfsen said...

Once again, CHG is not BE + ANE.

aniasi said...

@David

Can you tell me more about Satsurbalia? Google isn't giving me any information on it. In particular, why do you think is may have admixture from near India?

Davidski said...

There's no information anywhere what Satsurblia really is, since no one knows yet what it really is.

It's Basal Eurasian and something else Villabruna-like and MA1-like, and some of this might be from Central or South Asia, or not.

Impossible to say at the moment without more Paleolithic samples from Asia.

postneo said...

"without more Paleolithic samples from Asia" you make it seem as if theres a factory"

Davidski said...

OK whatever you say, but don't go all X files on us when more genomes are published and you don't have anything left to debate.

Matt said...

So, other (admittedly less) interesting stuff here:

aDna and Relevant to Europe / West Eurasia

http://smbe-2016.p.asnevents.com.au/days/2016-07-07/abstract/35599 - "The spread of farming across the Mediterranean to Iberia and its role in shaping ancient and modern European genomes" Valdiosera

"Here, we analyse new genome sequence data from 13 early farmers from Spain and compare them to previously published modern day and ancient genomes from Europe, North Africa and the Near East. We show that the first farmers to arrive to the Iberian Peninsula during the Neolithic, followed a coastal Mediterranean route bringing farming practices with them. These Neolithic individuals show a similar genetic structure across the North, North East and South of Iberia with no evidence of north African influence.

Furthermore, we observe a certain degree of genetic differentiation between Early Neolithic Iberian and Central European farmers. An indication of at least two founding populations of early Neolithic Europeans (one that arrived via the Mediterranean coast and the other via the Danube basin into Central Europe)."

"Among all early European farmers the Iberian Neolithic groups show the highest genetic affinities to present-day Sardinians suggesting that the modern population of the island are relatively direct descendants of these early Mediterranean farmers. "

"Finally, genetic similarities between Middle to Late Neolithic farmers from Ireland and Iberia potentially suggest the latter to be the origin of the Megalithic culture which spread along the Atlantic coast and later reached the British Isles and Scandinavia"

http://smbe-2016.p.asnevents.com.au/days/2016-07-06/abstract/35210 - "The genomic enigma of two Medieval North Africans" Gunther

"In this study, we present the genomic analysis of two human individuals from a cave site in the area of present-day Morocco which were directly dated to the Medieval period."

"Both individuals – which represent the first ancient genome sequence data from North Africa – do not exhibit particular genetic affinities to modern North Africans or any other present-day population in published genotype data sets despite relatively extensive data has been produced from many areas of Africa. In fact, the most parsimonious way to model them genetically is as two-source admixture between Mediterranean Europeans and Southern Africans. "

http://smbe-2016.p.asnevents.com.au/days/2016-07-04/abstract/35393 -

http://smbe-2016.p.asnevents.com.au/days/2016-07-04/abstract/35544 - "Signs of mobility and migration in the megalithic graves of Western Sweden?" Svensson

"We use the gallery grave at Torbjörnstorp as a model site for investigation of mobility. Here the individuals analysed all date to around 1800 BC cal, the second half of the Late Neolithic period in Scandinavia. However, the megalithic graves have been used for successive burials over a long time and even though the skeletal remains are fairly well preserved, the bones have been moved to make way for new burials and the bone material is often fragmented. The aDNA analyses can in this case be important for disentangling the demography of the individuals buried here, and coupled to isotopic results this can be used for discussing mobility patterns."

Matt said...

On European Neanderthal:

"Genetic analyses of five late Neandertal individuals" Hajdinjak

" To better understand late Neandertal populations and the interactions between Neandertals and modern humans we are investigating the genomes of European Neandertals from the time when they or their immediate ancestors could have met modern humans.

We identified five late Neandertal specimens – from the Troisième caverne of Goyet and Spy in Belgium, Les Cottés in France, Vindija Cave in Croatia and Mezmaiskaya Cave in Russia – where the fraction of endogenous sequences are between 6% and 64% after depleting microbial contamination through hypochlorite treatment. We have sequenced the nuclear genomes of these individuals to an average coverage between 1- and 2.7-fold."

"We further use these genomes to determine population structure among late Neandertals and their relationships to the Neandertals that contributed DNA to present-day humans, as well as to determine whether there was gene flow from early modern humans into these late Neandertals."

adna and World:
http://smbe-2016.p.asnevents.com.au/days/2016-07-04/abstract/35725 - "The Aboriginal Heritage Project: Reconstructing the Genetic History of Aboriginal Australia with Ancient DNA" Tobler

" The project leverages the unparalleled collection of 5000+ hair samples curated by the SAM along with cultural, morphometric and genealogical data, which were collated by Joseph B. Birdsell and Norman B. Tindale during extensive anthropological expeditions across Australia between 1926 and 1963. The broad geographic sampling and unique combination of ancient DNA and deep genealogies contained in the SAM collection provides perhaps our best opportunity to understand Aboriginal Australian genetic history prior to European colonisation. We present our outreach activities, which crucially involve re-consenting the hair samples through in-depth consultation with Aboriginal families and communities, along with preliminary phylogeographic analyses which reveal that pre-colonial Aboriginal Australia was characterised by deeply structured populations dating back to the initial colonisation of the continent."

Matt said...

Europe recent, fine scale for those interested in Finland and Estonia
http://smbe-2016.p.asnevents.com.au/days/2016-07-05/abstract/35643 -

"Large-scale whole genome sequencing of the Estonian population reveals novel loss-of-function variants and new insights into the population history" Metspalu

"Altogether 2244 whole genomes of geographically diverse individuals from Estonia were sequenced to a median depth of 30x using Illumina HiSeq with TruSeq PCR-free library preparation method. We found 19M SNVs and 6.6M indel variants with allele count larger than two and of which 8.4M were novel. Within this study we have analysed both loss-of-function variants revealed as well as the population structure of Estonia."

"To study the fine-scale genetic structure of the Estonian population, we concentrate on a subset of the genomes (N=436), which comprehensively cover rural Estonia to minimize the mixing effect of historical urbanization. We further combine these genomes with a pan Eurasian panel of high coverage genomes from hundreds of populations. Using haplotype and allele frequency based methods we show that the genetic structure within Estonia is largely in line with the division of inland vs. maritime Estonia what has been proposed based on archaeological findings. Furthermore, we identify and quantify the relative contributions of the three major genetic domains of the European gene pool in Estonians and estimate split times from linguistically and geographically adjacent populations. "

http://smbe-2016.p.asnevents.com.au/days/2016-07-06/abstract/35384 - "Fine-scale identity-by-descent and birth records in Finland provide insights into recent population history" Martin

World, recent:
http://smbe-2016.p.asnevents.com.au/days/2016-07-06/abstract/35338 - "The population history of Aboriginal Australia" Malaspinas

"We find that Papuan and Aboriginal Australian ancestors diverged long before Australia and New Guinea were separated by higher sea levels, suggesting early population structure in the ancient continent of Sahul (Australia, New Guinea and Tasmania). Moreover, all studied Aboriginal Australians are found to descend from a single founding population. As expected, we detect European and East Asian admixture across most of the modern Aboriginal Australian groups included in the study."

http://smbe-2016.p.asnevents.com.au/days/2016-07-05/abstract/35941 - "Out of Africa into Australia: an Aboriginal Australian genomic perspective"

" By comparing the SFS expected under alternative migration scenarios that explicitly take archaic introgression into account, we estimate that AA and Eurasians derive from a single OoA wave, but that the ancestor of these populations split from each other relatively early after the exit, some 51-72 kya. Additionally, we find evidence that East Asians share a common ancestor with Europeans rather than with AA. We estimate that the ancestors of these two separate waves of migration into Asia diverged 29-55 kya, with one wave leading to the colonisation of Sahul and the other one to the colonisation of East Asia."

Generally intriguing:

http://smbe-2016.p.asnevents.com.au/days/2016-07-05/abstract/35255 - "Re-evaluating the target of selection within FOXP2 suggests functional divergence among diverse human populations"

"Here, we comprehensively re-analyze FOXP2 with a high-resolution dataset comprising hundreds of next-generation sequenced genomes from globally distributed human populations. We test for fine-scale selection patterns both within the gene and between various human populations in order to resolve a hypothesis of recent positive selection. Intriguingly, haplotype networks and window-based Tajima’s D calculations indicate balancing selection in African populations."

"Strong evolutionary constraint amongst taxa but variability within Homo sapiens is compatible with this locus having a major functional role unique to humans."

Matt said...

Btw, off topic, came across these posts by Iain Mathieson on the use of SpaceMix and spatial genetics models to model the West Eurasian dataset from Laziridis and thought it might be of interest:

http://mathii.github.io/review/2016/01/25/spatial-genetics-1
http://mathii.github.io/2016/04/30/joint-visualization-of-spatial-and-genetic-structure

"Above, you can see the geographic locations of the samples, as well as the first two principal components. Basically, the North-West African samples are very differentiated by the PCA, and the rest of the samples look, at least qualitatively, like a map of Europe, as expected.

###SpaceMix I ran SpaceMix with and without spatial priors (i.e. using the true locations of the samples as priors for the geogenetic distance), and it didn’t seem to make much difference. Here’s the result of the SpaceMix analysis, compared with PCA (95% credible ellipses).

Basically what SpaceMix is doing is finding positions for populations in some theoretical “geogenetic” space, such that the genetic correlation between populations is proportional to the geogenetic distance."


The structure has some differences between the PCA and SpaceMix (see Europe in the SpaceMix and you have some quite different positions for the Bulgarian, Hungarian, Croatian populations than in PCA).

SpaceMix supposedly contains more information than two PC1 and PC2 dimensions - http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005703 - "An advantage of PCA is that it can explain more complex patterns of population structure by allowing up to K different axes. Although SpaceMix can easily be extended to more than two dimensions, simply by allowing Gi to describe the location of a sample in d dimensions, interpretation and visualization of these higher dimensions is more difficult, and so we have stuck to two dimensions. On the other hand, SpaceMix can describe in two dimensions patterns that PCA, due to the constraints of linearity, would need more to describe."

Anyone have any opinions on what is going on there?

Grey said...

@Matt

Interesting stuff, ty.

Davidski said...

I have to say though, I'm somewhat disappointed in the abstract selection considering it's 2016 and with ancient genomics where it's at now. I was expecting more stuff with ancient data from all over Asia.

Davidski said...

Anyway, my prediction is that the Ganj Dareh farmer girl will show surprisingly high South Asian admixture in ADMIXTURE analyses, but, at the same time, low Ancestral South Indian (ASI) affinity, as represented by the Onge and/or Dai.

That's because a large portion of South Asian ancestry dating to the Neolithic is probably derived from the eastern part of the Fertile Crescent, in other words the Zagros Mountains.

aniasi said...

@David

Do we know where or when the Satsurbalia sample comes from?

Davidski said...

Satsurblia is an Epigravettian sample from Satsurblia, western Georgia, dated to ~13,200 years before present.

You should read the two papers in which it was analyzed (although keep in mind neither really hit the nail on the head).

http://eurogenes.blogspot.com.au/2016/05/the-genetic-history-of-ice-age-europe.html

http://eurogenes.blogspot.com.au/2015/11/fourth-strand-of-european-ancestry.html

Rob said...

The paper from the site context itself is

"Satsurblia: New Insights of Human Response and Survival across the Last Glacial Maximum in the Southern Caucasus"

Care of Google

aniasi said...

@David

Thanks. For some reason it doesn't show up when you type it into Google, but Kotias does.

Chad Rohlfsen said...

Having more BE via Natufians, plus having a shift towards ANE away from WHG would create the same scenario of being further from Europeans than CHG.