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Wednesday, June 10, 2015

101 ancient Eurasian genomes (Allentoft et al. 2015)


It'll take me a while to digest all of the information in this massive new Allentoft et al. paper. But I've already noticed that, just like in Haak et al. 2015, the Yamnaya samples are again from the eastern half of the Yamnaya horizon. This time, however, not all of the Yamnaya individuals carry Y-haplogroup R1b; one of the five samples belongs to Y-haplogroup I2a (see here).

So I'm wondering what more westerly Yamnaya sites will reveal in the future, considering the predominance of Y-haplogroup R1a among the Corded Ware individuals sampled to date, and the close genome-wide relationship between the Yamnaya and Corded Ware?

Abstract: The Bronze Age of Eurasia (around 3000–1000 BC) was a period of major cultural changes. However, there is debate about whether these changes resulted from the circulation of ideas or from human migrations, potentially also facilitating the spread of languages and certain phenotypic traits. We investigated this by using new, improved methods to sequence low-coverage genomes from 101 ancient humans from across Eurasia. We show that the Bronze Age was a highly dynamic period involving large-scale population migrations and replacements, responsible for shaping major parts of present-day demographic structure in both Europe and Asia. Our findings are consistent with the hypothesized spread of Indo-European languages during the Early Bronze Age. We also demonstrate that light skin pigmentation in Europeans was already present at high frequency in the Bronze Age, but not lactose tolerance, indicating a more recent onset of positive selection on lactose tolerance than previously thought.

Allentoft et al., Population genomics of Bronze Age Eurasia, Nature 522, 167–172 (11 June 2015) doi:10.1038/nature14507

See also...

Population genomics of Early Bronze Age Europe in three simple graphs

ADMIXTURE analysis of Allentoft et al. and Haak et al. ancient genomes

728 comments:

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Davidski said...

The figures and tables are available here.

http://www.nature.com/nature/journal/v522/n7555/fig_tab/nature14507_ft.html

The supp info is here.

http://www.nature.com/nature/journal/v522/n7555/full/nature14507.html#supplementary-information

bellbeakerblogger said...

I see the bar plots in Fig.6 I'm still trying to figure out where the individuals come from.

In any case, Remedello I is definitely Neolithic and looks like a lot like Sardinian and Trelles individuals, which honestly is not surprising.

Again, every swinging **** Bell Beaker was mixed with Corded Ware folk. There is no island and no continent where they weren't mixed, and above all, Central Europe where the only BB genomes come from. Even the earliest Portuguese Beakers probably had Peninsular Corded influence. So I'm not quite sold on BBC and CWC being two peas in a pod.

bellbeakerblogger said...

In other words, the lesser Yamnaya or ANE like influence so far detected in BB, more than likely is because they are at least half Battle Axe in their ancestry. More than any place, this would be especially true on the Elbe and Mittel-Saale

Colin Welling said...

Amazing!!!

More samples of bell beakers and they all come back r1b. Also, we now have an r1b sample in Corded Ware even though they mostly come out r1a.

Also, here is what they say about androvono "The enigmatic Sintashta culture near the Urals bears genetic resemb- lance to Corded Ware and was therefore likely to be an eastward migration into Asia. As this culture spread towards Altai it evolved into the Andronovo culture (Fig. 1)"

Colin Welling said...

also, once again we have r1b being dominant in yamnaya. I think its getting clear that yamnaya were r1b, their was a minor input of yamnaya into the closely related corded ware, and corded ware then moved east and replaced most of the r1b on the steppe along with spreading IE culture eastwards.

Also, Bell beaker is not corded ware derived but yamnaya derived, albeit closer to farmers than the yamnaya themselves which is probably due to mixture with locals and the fact that bell beaker comes from the western yamnaya.

Roy King said...

Fascinating! It will be important to determine whether the R1b among BA Armenians is Z2105 or not. The R1b is well before the Armenian language, but BA Armenia has a large "Teal" component like Yamnaya. We should also determine if the BA Armenian is V13 or M123--makes a huge difference. The Iron Age J2s--J2a in Altai and Russia and J2b in Armenia fit with a later J2 expansion, like J2a1b in BR2 Hungary. BA Armenians do appear to be a palimpsest of Neolithic farmers sharing with EN Europeans and contemporary Sardinians and Chalcolithic N Italians.

Mike Thomas said...

Which table is the Y data on ?

Vincent said...

The E1b1b guy was M123 or V22 for sure

Mike Thomas said...

Ok this is whack
Copper/ Bronze Age italy was full of I2 ?!
Must have been replaced by later migrations from Central Europe and greece

Mike Thomas said...

Iron Age russia full of J2
So long to traditional explanations of Scythians
Looks like it was the other way round- they came from South of caucasus

Davidski said...

The earlier Scythian samples from Keyser et al. are all R1a.

So the J2 is due to acculturation of a new population in the region.

Skilur said...

@Mike Thomas
Not really, most Scythian samples still were predominantly R1a. Scythians were nomads who migrated quite much and during their migrations they mixed with other populations and picked their dna/y-DNA. I would be even not surprised if they found Y-DNA L or G in the iron age steppe originating from Saka tribes who spent some time in South Central Asia and migrated back.

Mike Thomas said...


But the "early Scythians " of the bronze age *aren't actually Scythians*.

They formed in the Iron Age

Mike Thomas said...

The say

"Using D-statistics, we find that Corded Ware and Yamnaya individuals form a clade to the exclusion of Bronze Age Armenians (Extended Data Table 1) showing that the genetic ‘Caucasus component’ present in Bronze Age Europe has a steppe origin rather than a southern Caucasus".

truth said...

@ Mike Thomas

There is no replacement. The I2 is typical of neolithic farmers, and it is a lineage that comes from the mesolithic. This sample from Italy is close to Sardinians and thus neolithic farmers. Nothing strange.

Davidski said...

Mike, the Scythian samples in Keyser et al. are from the Iron Age.

Mike Thomas said...

Oh ok

Truth:
Yes my point is there must have been massive replacement *after the early bronze age* in Italy.

Roy King said...

@Mike Thomas
I wonder whether the J2a's in Russia are due to Greek Crimean/Caucasian colonies that traded with locals during the Archaic (Iron Age) period?

Mike Thomas said...

And the lack of G, F, EV13, admittedly low sample number, highlights some theories on the Neolithicization of italy

Mike Thomas said...

Roy
Maybe!
although my initial impression is to doubt that the greek colonies had a significant impact demographically; esp beyond the towns themselves

I think it's clear links of "Scythians" of Russia and the real Scythians on the edge of the near eastern civilisation (Assyria, Persia)

Davidski said...

What I find interesting is that Corded Ware are R1, R1a and R1b. On the other hand, the (eastern) Yamnaya are basically R1b.

No idea what that R1 is yet, but it'll be interesting to see Y-DNA samples from pre and proto-Yamnana cultures, like Khvalynsk and Repin.

Shaikorth said...

The Iron Age Russian samples are from Southern Siberia and have affinities to modern Siberians despite being J2. There's also J2a in Iron Age Altai which is broadly similar. Greek relation seems unlikely, but modern Central Asian J2 might be worth a comparison.

Skilur said...

@Davidski
What is your opinion about Sintashta/Andronovo? Can you already say which modern population resembles them most? Would you still say that they have an origin in eastern Yamnaya?

Davidski said...

It's hard to say much at the moment. I'll have to look at the genomes first hand.

Annie Mouse said...

Nice summary in the supplementary material (BAE= Bronze Age Europeans)

"In summary, our results suggest the following interpretations:
- Predominantly West Eurasian ancestry for BAE, with the exception of some later BA individuals from Asia, which show influence of ancestry related to present-day Siberians
- A gradual decrease in West-Asia / Neolithic farmer related ancestry from Southern and Central BA Europeans towards the North, which is also present in Armenians but absent from the Northern Caucasus (Yamnaya).
- An opposing gradient in Caucasus / steppe related ancestry, maximized in the Yamnaya and distantly related to Native Americans. Possibly due to the presence of MA1-related ancestry in the Northern Caucasus.
- A genetic link between the Kalash and the steppe through Yamnaya-related people.
- Native American-related ancestry in the Okunevo, possibly due to shared ancestry with paleolihic hunter-gatherers from Mal’ta."

Chad Rohlfsen said...

These Beakers look more Yamnaya-like than the last bunch.

Kurti said...

Iron Age Altais and Iron Age Russia full of J2. "acculturated other groups" my a$$ :D

This is clearly the geographic distribution of Scythians.

I said it in the past and will say it again. Scythians were a mix of R1a*, J2a and some other Haplogroups such as R1b/R2 LT*, G just like any other Indo_Iranic tribe. It gets obvious if you look at the Haplogroup distribution of modern Indo_Iranic speakers. It can't be "acculturated" Haplogroup if it exists among all branches of the Indo_Iranic family.

The Bronze Age individual might have been one of them.

Kurti said...

Bronze Age individual from Hungary might have been one of the Indo Europeans too.

59ea7626-0fc9-11e5-9e33-fb42f703675e said...

No N paternal haplogroups?

Mike Thomas said...

Stating the obvious - this study is great
Excellent sample set, and makes well substantiated conclusions

It shows clearly what I've been suggesting - whilst the process of PIE began in the early Bronze Age; it was an ongoing affair- as late Iron Age still unfurling. And there were clearly more complex admixture processes than single-origin ones

Romulus said...

Look at that lactase persistence in the Yamnaya! Would be interesting to know the context of the I2 Yamnaya.

Mike Thomas said...
This comment has been removed by the author.
Vincent said...

@Roy King

The E1b1b guy is M123*(xM34)

Kurti said...

Bronze Age Sintashta is slightly closer to West and EVEN South Europe than East Europe nd BrArmenia.

However with Andronovo it's a different case. This is closer to BrArmenia and East Europe.


man ancient DNA is so confusing.


http://www.nature.com/nature/journal/v522/n7555/fig_tab/nature14507_SF5.html

Roy King said...

@Vincent
Yes, that's great! The Armenian is M123(xM34). Likely a relic from the Fertile Crescent Neolithic!

Skilur said...

@Kurti
Scythians were Post-PIEs so non-R1 lineages among them are not surprising in any way. Anthropological studies showed that southern Saka resembled modern Pamiri and were different from the more "european-like" and more northern living Iranians. Scythians in the Caucasus resembled modern Caucasians to a large extent also and the Siberian Iranians were quite siberian/uralic shifted if I am not wrong. So they were not just the descendants of Proto-Indo-Iranians even when they were extremely close to Proto-Indo-Iranians.

Davidski said...

Mike,

The R1, R1a and R1b in Corded Ware is definitely not from CT or any other farmers like GAC.

It's probably from Repin, which was largely of EHG origin, and might have spawned both Yamnaya and Corded Ware.

Mike Thomas said...
This comment has been removed by the author.
Kurti said...

@Roy King

If it was due to "colinies" in East Europe, how are we going to explain the appearance in Iron Age Altais? Obviously no Greek colonies. Both places known as Scythian settlements. When the Indo_Iranic people formned and especially when the Scythian formed. The must have belonged to various Haplogroups. We know from a study that the Alans from East Europe were mostly G2a as example.

Kurti said...

Shaikorth

"The Iron Age Russian samples are from Southern Siberia "

Such as Kazakhstan, which is well known as Iron Age, Indo_Iranic settlement.

Davidski said...

"Repin was small scale nothingness"

Indeed, and most Europeans are the paternal descendents of just three men who lived during the Eneolithic.

CT was too big and probably had too much diversity to be PIE.

la señora bibiloni said...

A reference to CT, at last!
Let's keep in mind that PIE is a reconstruction, so there could be different "dialects" of what we call PIE... I can't possibly believe that I can get into a time machine and arrive to a time and place where they speak PIE just as it was reconstructed.

Kurti said...

@Skilur

This "mixture" must have happened within the early stage of Indo_Iranians, because those Haplogroups are uniformly found among every branch of this linguistic group.

If it was later "addition" from differen't source, you would expect one group in the Caucasus for example to have high frequency of a Haplogroup which the other lack and vica versa.

But thats not the case. Haplogroup J2 is a significant Haplogroup in Iranic speakers from SOuth_Central Asia all the way into West Asia and the North Caucasus. The same is the case with G and R1a.

Therefore this can't be later "addition". It must have been part of the original Indo_Iranians.

And you might have missed that the J2 was actually found in Iron Age South Sibieria and Altais.

Davidski said...

la señora bibiloni,

There was a massive invasion of Europe from the east during the Corded Ware period.

Massive invasions and population replacements result in language shifts.

And the population doing the invading was not similar to the typical European farmers of East Central Europe. So what language did this eastern, atypical, non-CT-like new group speak?

It wasn't Uralic, because that came through the Forest zone much later.

Davidski said...

Kurti,

If J2 expanded in Central Asia only during the Iron Age, then it wasn't a feature of the earliest Indo-Iranians.

Come on.

Nirjhar007 said...

But J2 is related to Indo-Europeans...

Mike Thomas said...

Well, there certainly appears to be a radiation of J2 during the mid-late Bronze and iron ages, when PIE was being consolidated in the places where it is first attested- Greece, Anatolia, Indo -Iranian lands, Italy..../

Romulus said...

Given that they make the connection that the success and westward expansion of the Yamnaya is derived from a cultural/technological package learned from Mesopotamia it would seem to imply that the "teal" component in the Yamnaya was input from ancient Mesopotamia itself.

Nirjhar007 said...

Am i reading this right BA andronovo has I2???

Joshua Lipson said...

What's the date of the Armenian E-M123?

Kurti said...

"If J2 expanded in Central Asia only during the Iron Age, then it wasn't a feature of the earliest Indo-Iranians.

Come on."

It must have been, Otherwise you would expect this Haplogroup to lack in some branches.

Since it is found among all Indo_Iranian branches in significant percentage it must be a native part of them.

There is no other explanation for that.

Just as example if you have green eyes, all your siblings have green eyes, and your niece (the daughter of your brother) has green eyes too. What is more likely, that she inherited this from your bro or his wife?

J2 is strong in all Indo_Iranians even those living isolated in the Pamir Mountains, heck even Uygurs in West China.

Kurti said...

And another strong evidence for that. J2 appears on the scene only with and after the supposed Indo Europeans expansion. No J2 on the World Map prior to Bronze Age.

I think at least after thoe results people should start to accept that J was part of the migration.

Davidski said...

Nirjhar,

The Andronovo and Sintashta samples are R1a. We might soon learn if they're ancestral to South Asian Z93.

Romulus,

It's highly unlikely that the teal component actually came from Mesopotamia. It's most likely a young composite from the north or west Caucasus.

Nirjhar007 said...

David We need aDNA from more Southern areas to conclude anything:) but it will be Interesting though....

Skilur said...

@Kurti
Not all are rich in J2 Pashtuns have just around 5% of it. All Indo-Iranians(except of some Indians) today populate regions where Neolithic Farmers lived once so they have a similar near eastern-related substrate. Andronovo/Sintashta will have no J2 maybe I2a, N or R1b but certainly no J2.

la señora bibiloni said...

Davidski, I agree with you that Corded Ware (expanding to the west) and Andronovo (to the east) spoke languages derived from what was spoken in Yamna, whatever language it was. My comment was about CT being "too large" (in population, I assume) to be the PIE homeland, and that maybe the CT people (and Sredny Stog too) could have spoken different dialects or variations of what we call PIE.
Following Mallory, I don't think PIE was the language of a nomadic pastoralist population, it has too many agricultural and architectural terms for nomads. But I haven't found a fully convincing theory yet.

Nirjhar007 said...

David and others,
Can you please link where the full list of Hg's with samples are given:)

Davidski said...

There is no list. We'll have to work it out from the bam files.

Nirjhar007 said...

This is just not cool:)....

Grey said...

mostly messing but

if old near eastern was E1 (of one or more kinds) and they were mostly replaced by X from somewhere adjacent to the Himalayas who moved into the near east and became a new near eastern (and then also moved on from the near east into Europe) and who also moved onto the steppe east of the Caspian mixing with the steppe R1 component to become incorporated into PIE and then some of that R1b PIE moved into Armenia then you might end up with

Yamnaya = steppe + new near eastern
Armenian = yamnaya + old near eastern
Iraqi Jews = old near eastern + new near eastern

mostly messin' but just thinking about how multiple populations could be 50% similar to each other by being 100% on one branch of admixture and 0% on another.

Grey said...

"and they were mostly replaced by X from somewhere adjacent to the Himalayas who moved into the near east and became a new near eastern"

meant to be

...and they were mostly replaced (except in refuges like Armenia) by X from somewhere adjacent to the Himalayas who then moved into the near east and became a new near eastern...

Davidski said...

Why the Himalayas?

North and/or West Caucasus sounds more plausible.

Grey said...

@Romulus

"Given that they make the connection that the success and westward expansion of the Yamnaya is derived from a cultural/technological package learned from Mesopotamia it would seem to imply that the "teal" component in the Yamnaya was input from ancient Mesopotamia itself."

Does that follow? Couldn't it simply mean they had something to trade (horses, copper?) and the thing(3) they had to trade were responsible for the success and westward exapnsion?

Grey said...

Davidski

"Why the Himalayas?"

Pet theory based on evidence too circumstantial to say out loud :)

"North and/or West Caucasus sounds more plausible."

I agree on the face of it (and it's my option 2).

Romulus said...

@Grey

Given that our initial Samara R1b1 EHG was mostly HG/Malta like at 5,000 B.C. I don't see any other better candidates for the input.

Romulus said...

They really did a shit job on the Y DNA analysis. Was that intentional?

capra internetensis said...

Yes, Romulus, they deliberately did a bad job for some nefarious reason, then released all the data to the public so that they would be found out immediately.

Davidski said...

It is strange that they didn't even include a table with the Y-HGs listed for each sample, as far as I can see anyway.

Colin Welling said...

Yes, that is annoying since i would like to match each ydna with not just a culture but also a country to say the least.

Anybody know more on this Stalingrad Quarry, r1b, guy. He is not listed as yamnaya but he is in the center of the yamnaya world in both space and time.

Mike Thomas said...

they have a nice table of mtDNA results in the Supp., but not Y DNA.
Odd. .

Colin Welling said...

I haven't been following the near eastern admixture in yamnaya too closely but has this paper helped to sort out the matter of where that component came from and how it relates to the typical, sardinian like, farmer ancestry in europe?

Based on a quote mike picked out it sounds like that might have been the CT culture. Mike, what was the time frame for the CT input into the steppe populations?

Krefter said...

I added Y DNA frequencies to my spreadsheet. Don't know how many of the males they found a Y DNA haplogroup for.

https://docs.google.com/spreadsheets/d/1HuNPykGuq2PbHkUOL5dCiwrveIy-OGO2qOklwfsayW8/edit

Mike Thomas said...

Colin
There is evidence for exchange as early as 5000 BC (ie pre-pre-Yamnaya period). But it apparently poured in just prior and c. 3000 BC, as C-T disintegrated (ie spread out all over central, eastern (esp. steppe) & Southeastern Europe.

Davidski said...

The southern ancestry in the Yamnaya sampled thus far, from east of the Don, isn't from CT or any typical early European farmer group. It's almost certainly from the Caucasus and/or surrounds.

But Yamnaya from west of the Don might well have some CT and GAC admix. Hence, this might be why Corded Ware and Sintashta show it.

Colin Welling said...

If the later is true then they may be a candidate for the "new neolithic" in yamnaya. Are you sure it was 3000bc and not a little later. Because at 3000bc it would be difficult to homogenize such a component across the yamnaya horizon but possible. Any later and we are no longer talking about a group that fused with the yamnaya, but invaded the already established yamnaya.

Kurti said...

@Skilur

Exceptions confirm the rule. Look at all the Indo_Iranian tribes around them. So what can the Pashtuns prove anyways. Thats pocking for mistake in an almost perfect scenario, Ossetians are the only Indo_Iranian group with close to 2% R1a. Claiming R1a is not part of the Indo_Iranian tribes would be ridiculous.

Also all DNA studies I have seen on Pashtuns shows at least 8% J2. But than even 5% is significant.

jackson_montgomery_devoni said...

Does anyone know exactly which Iron Age cultures these J2 and J2a samples come from in Russian and Altai?

Davidski said...

Here's a comment by David Anthony on the southern admix in the Yamnaya sampled to date. I think it's a reasonable assessment for now.

"On the "Caucasian" element in Yamnaya: Sasha Khokhlov in Samara and Sasha Kozintsev in St Petersburg, both biological anthropologists, have described a narrow-faced skull type that is often labeled 'Mediterranean', but both have documented that this type existed as a native element in the steppes at a very early era, and it was not really classic 'Mediterranean'. This type could represent a southern steppe population that already existed in the Mesolithic, linked to Mesolithic populations in the North Caucasus. The genetic element in Yamnaya that seems to come from a Caucasian population was present earlier at the Eneolithic Khvalynsk cemetery. This is not yet published. The mysterious Caucasian element is about 25% of the ancestry of Khvalysnk, but it rises to 50% of the ancestry of Yamnaya. Perhaps the additional increment of Caucasian genes came through increased marriage between Maikop and steppe people after Maikop introduced wheeled vehicles to the steppes (???)."

Kurti said...

" today populate regions where Neolithic Farmers lived once so they have a similar near eastern-related substrate. Andronovo/Sintashta will have no J2 maybe I2a, N or R1b but certainly no J2. "

There is still someone here who thinks J2 is a Neolithic farmer lineage !?

Proto Indo Iranian is Andronovo+BMAC.

jackson_montgomery_devoni said...

There is a possibility that J2 may be a Neolithic farmer lineage that originated in the Zagros area or a bit further east I think.

Mike Thomas said...

David

Interesing

Colin

Well, yes it might have extended to later, of course. In fact, most likely in the first quarter to mid second Mill BC.
But I agree with David, Im not suggesting CT expansion reached all the way to north central Asia.

Nirjhar007 said...

Kurti,
//Proto Indo Iranian is Andronovo+BMAC.//
Add SSC also anyway we should wait to see more aDNA.....

Nirjhar007 said...

but sorry i don't consider Andronovo to be Indo-Iranian its too late and highly unconvincing, that culture is related to Proto- Scythian type of people...

Grey said...

Low level of LP implies dramatic rate of increase in north western Europe.

If it was selection pressure then you'd think selection pressure on that scale ought to have spread further in southern and eastern Europe by now unless the advantage was specific to the northwest region in some way i.e. climate i.e. crop yields i.e. calories.

so maybe
Southern Europe = wheat
North Eastern Europe = millet
North Western Europe = milk

Nirjhar007 said...

Krefter, i'm unable to see the Y-DNA:).

Grey said...

Davidski

Just to translate my statement "I agree on the face of it (and it's my option 2)" - if something boils down to two options I always prefer to pick the longer odds one for fun.

Krefter said...

@Nir,

I don't know what to say. Can you see the speadsheet at all? Anyways, here's the Y DNA. I don't know how many samples successfully found their Y DNA haplogroup. I just listed the number of males from each group.

Yamnaya=5: R1b 80%, I2a 20%.
Stalingrad RUssia=1: R1b 100%.
Armenia BA=3: R1b 66.7%, 33.3% E1b.

Central Asia:
Sintashta=2: R1a 100%
Androv=1: R1a 100%.
Karasuk=3: R1a 75%, Q1a 25%.
Mesh=2: R1b 50%, R1a 50%
Gora=2: R1a 100%.

Central-North Europe.
BBC=4: R1b 100%.
CWC=7: R1a 66.7%, R1b 16.7%, R1 16.7%.
Scan BA=8: R1b 50%, I1 33.3%, R1a 16.7%

Other Europe:
HungaryBA=6: I2=50%, I2a=25%, G2a=25%.
North Italy=3: I2=66.7%, I2a=33.3%

Iron age.
irArm=1: J2b 100%.
irAtali=??: Q1a 66.7%, J2a 33.3%
irRus=??: J2 100%.


Krefter said...

The I1, R1b(U106, L238, DF19, DF99?), and R1a together in Late Neolithic/Bronze age Sweden/Denmark support the idea proto-Germanic developed around south Scandinavia, northern Germany, and the Netherlands. I1 hasn't been found anywhere else, except Neolithic Hungary.

Krefter said...

Here's a link to Y SNP calls of the BA Armenians. I checked one of the R1bs, and he's L23! So 4,000 years ago R1b-L23 was at least in Russia, Germany, Scandinavia, and Armenia.

http://www.anthrogenica.com/showthread.php?2120-quot-DNA-and-the-Origins-of-Peoples-The-Armenians-quot-Lecture&p=88530&viewfull=1#post88530

Krefter said...

I'm using ISOGG Y-Tree AddOn on the BA Armenians right now.

Krefter said...

SAMEA3325421 a Bell Beaker man from Germany is R1b-U152.

http://www.anthrogenica.com/showthread.php?4640-Population-genomics-of-Bronze-Age-Eurasia-(Allentoft-et-al-2015)&p=88630&viewfull=1#post88630

Nirjhar007 said...

Krefter yes i see them now:) there was a problem before BTW please give the R1a from Sintashta:).

Krefter said...

Here's an analysis of the ancient Armenian Y DNA using ISOGG Y-Tree AddOn.

https://docs.google.com/document/d/1Txjf7qEHsRUu9-o5KpKJvLAF465gr4HBekzcX__Y2hU/edit

@Nirj,
"Krefter yes i see them now:) there was a problem before BTW please give the R1a from Sintashta:)."

I don't, but we should learn in the next few days. Here's the ANE K7 results of a Sintashta individual.

http://www.anthrogenica.com/showthread.php?4640-Population-genomics-of-Bronze-Age-Eurasia-(Allentoft-et-al-2015)&p=88565&viewfull=1#post88565

Just a little less ANE than Samara Yamnaya, more ENF and ASE, and less WHG. He'd probably score around 30% or less WHG in ANE K8, unless not enough SNPs were used in the ANE K7 results.

Mike Thomas said...

Krefter

"I'm using ISOGG Y-Tree AddOn on the BA Armenians right now"

Are you saying people have starting sifting through the BAM file and transforming into recognisable SNPs ?

Simon_W said...

Looks like a fantastic new paper! I can't wait to devour all the new evidence. Too bad I got to work now...

Krefter said...

@Mike,

They must be. I checked Felix's site. He hasn't made any posts about work on Alentoft genome. BTW, the Bronze age Montengero man is clustering in SouthEast Europe. Almost all LN/BA are in central Europe. Not consistent with Haak genomes.

Davidski said...

"Not consistent with Haak genomes."

We'll see about that.

Mike Thomas said...

Krefter

Are you saying that the BA Mtn specimen cluster with modern SEA autosomally, or from Y perspective ?

And- "almost all LN/ BA are in Central Europe.."
Again, are you talking about autosomally, and compared to moderns ??

Mike Thomas said...

actualky Karl, they intimate that all this was set off by other social and demographic mechanisms. So it wasnt "first from the steppe".
The steppe movements wer secondary; and there were other tertiary and quaternary movements

Krefter said...

@Mike,
"Are you saying that the BA Mtn specimen cluster with modern SEA autosomally, or from Y perspective ?"

They cluster in SouthEast Europe in a PCA from Figure 1.

http://www.nature.com/nature/journal/v522/n7555/fig_tab/nature14507_SF1.html

No dates were given. One is labeled as Late Bronze age and another Iron age. The PCA looks messy though. We'll have to wait for genome blogger's analysis.

Karl_K said...

@Mike

Obviously. But you could say the same thing back to the beginning of time. Actually... this was just part of a mass migration from Africa.

I was only referring to Marnie's particular concern about the directions that people were moving within this time period. Saying that Indo-European languages didn't spread to Europe via a mass migration from the Steppe is looking quite absurd with the data at hand.

Krefter said...

It looks like West Eurasian diversity that exists today mostly existed in the Bronze age(at least in Armenia, North Europe, and Montenegro?.. SE Europe?).

Mike Thomas said...

Lol yes Karl, I take your point
There was definitely migrations from Eastern Europe, including the steppe.

But I await the absence of any curve balls from the pending Bronze Age greece study to undeniably link it with PIE.

Alexandros said...

Although I was among the very few anticipating emergence of J2 linages among these new samples, now that we eventually have them, I really do not know what to make of them!! Their location is absolutely surprising to me. I see people rushing to link these J2 samples with the Scythians and others with Neolithic farmers. I prefer to remain undecided at this point. What puzzles me is the high frequency of J2 in Crete and Cyprus (around 25-30% in both islands). If J2 was a Central Asian haplogroup, you would need a massive migration from there into these two islands. The same applies to the scenarios putting the origin of J2 somewhere in the Caucasus. I am not sure if we can support such migrations archaeolgically. Probably not. We can support a migration from Anatolia to Cyprus (and maybe Crete) during the early Bronze age however. What we cannot be certain is whether J2 was already present in the Eastern Mediterranean islands before the Anatolian migration, or whether this migration brought the J2 along.

Another interesting finding for me is the E1b1b in BA Armenia. I beleive if we find out the subclade of this haplogroup (M123, V22, V13?) it will reveal tons about the presence of E1b1b in ancient southeast Europe. My guess is that this will be a V13, but I have noticed people doubting this. I do not know why..

Mike Thomas said...

Alex

I'm putting some $ on V13. But if so, why and how did it disappear from the near East between the Bronze Age and now ?

Abiut greek islands : Id be cautious as to making inferences from island populations. To me they seem the opposite of relict areas

Krefter said...

@Alexandros,

The ArmenianBA E1b is M123.

https://drive.google.com/open?id=1Txjf7qEHsRUu9-o5KpKJvLAF465gr4HBekzcX__Y2hU&authuser=0

Alberto said...

I still need to read the paper carefully, but one thing no one has commented about: The Afanasievo samples seem to be almost exactly like the Yamnaya ones. Yet, they are contemporary (or Afanasievo might actually be older). And they are from places some 2000-3000 Km. away.

Isn't this a bit odd, when Yamnaya was a mix of 2 quite different populations? Did the exact same mix of the exact 2 different populations happen at the same time in such distant places? Or once the mixing finished (after a 1000 years process) this new population moved really fast? And if so, in which direction, Yamnaya->Afanasievo or the other way around?

Nirjhar007 said...

Mike, we still need some good amounts of aDNA from Balkans before arguing anything confidently for Europe right?

Davidski said...

Alberto,

I'd say that both the ancestors of the Afanasievo people and the Tarim Basin mummies, who might well have been one and the same, left the European steppe before Yamnaya proper came into being.

I'm betting they were the Repin people, who also helped to form Corded Ware. But who really knows? We need more ancient genomes.

Nirjhar007 said...

Alberto,
'' Yamnaya->Afanasievo or the other way around?''
Interesting i actually suggested more about homogeneous population between the Central Asian and East European rather than movements from A->B or B->A , if we had aDNA from neolithic that would have been gold...

Alexandros said...

@Krefter
Thanks, that's great! Where did you find this info?? So M123? That's intriguing.. My first thought then is that M123 might have been a (minor) subclade of the Neolithic diffusion, at least the difussion from the Levant to North Anatolia. I am not saying that this is a fact. Still need to get my head round it..

@Mike
I see your point about island populations, however note that both Cyprus and Crete are large islands with nearly 1M population each. Yes bottlenecks and genetic drifts are likely, but on the other hand it may happen that they escape some of the migrations affecting the mainland. Look at Sardinia for example..

capra internetensis said...

@Alberto

The Afanasievo samples are all radiocarbon dated from ~3100 to ~2800 BC (give or take a century or two), while these Yamna samples (of which 3 are dated) have central dates of ~3000 to ~2500 BC, give or take about 350 years (!). So these Yamna samples are probably a little younger than the Afanasievo ones. The Haak et al Yamna samples, OTOH, are almost exactly the same age range as these Afanasievo ones.

Mike Thomas said...

Alberto/ David

"'Id say that both the ancestors of the Afanasievo people and the Tarim Basin mummies, who might well have been one and the same, left the European steppe before Yamnaya proper came into being.

I'm betting they were the Repin people, who also helped to form corded ware .."

Good initial point Alberto. The Afansievo is at least contemporary, if not older. And whilst possible, I don't buy the Repin explanation, for the obvious reason that they were at best incipient pastoralists; and lacked the social -cultural and demographic means to achieve such a mugration feat.

Nirj:
Of course we need DNA from the rest of eurasia. To me, the cumulative data suggests that the northern most areas were susceptible to massive population fluctuations. By the BA a massive chunk of northern west eurasia was more or less homogeneous, **geneticaly**. But does this = PIE ??!

Nirjhar007 said...

Too bad we don't' have the Y lineages from Afanasievo! BTW Capra, what will be your theory on this resemblance?:)

Davidski said...

Mike,

Repin is often seen as early Yamnaya. Even more primitive yes, but that doesn't mean they couldn't move far.

http://eurogenes.blogspot.com.au/2014/12/pit-grave-yamnaya-kurgans-are-as-old-as.html

The Tarim Basin mummies were without a doubt largely of European ancestry.

Nirjhar007 said...

Then they had R1a-Z280's right?:D

Krefter said...

Geneticker is posting the Y-results.

https://genetiker.wordpress.com/2015/06/11/y-haplogroups-for-prehistoric-eurasian-genomes/

For sample reference.

https://drive.google.com/open?id=1HuNPykGuq2PbHkUOL5dCiwrveIy-OGO2qOklwfsayW8&authuser=0

See the R1b1a2 in Bronze age Siberia. Must be from admixture with R1b1a2-rich people back when they were near Yamnaya territory.

Mike Thomas said...

Dave
True
First of all, that study is sloppy as it lumps half of west eurasia as "Yamnaya", as well as very early forms which are too premature to call Yamnaya. For now, I'm taking Rassamakins word on chronology; and whatever the case, the secondary nature of Yamnaya phenomenon is clear to eveyone in the know; including the learned authors of the study we're presently discussing

My only critique is , without actual neolithic samples, we're no closer to solving the same debates we've been having for 3 years.

Yes, the tarim mummies might well have been european, indeed, or at least partly so.

Alexandros said...

Thanks Krefter, great!

Davidski said...

Nirjhar,

R1a-M417 is an European marker. So the Tarim Basin mummies need not have belonged to R1a-Z280.

Krefter,

Okay, but for everyone's benefit here, let me just say that Genetiker is a bit of a fruitcake, and cannot be seen as a reliable source.

Nirjhar007 said...

Mike,
// tarim mummies might well have been european, indeed, or at least partly so.//
Partly at its peak.
Krefter,
DE ? DE from Armenia??
BTW good stuff have to keep an eye on....

Nirjhar007 said...

Dear David, Without any data from Say SC Asia, BMAC, Northern Iran-Kurdistan etc etc we should not make such conclusions....

Aram Palyan said...

Nirjhar that DE is not correct imho.
Armenian aDNA, one E1b1, one J2, and 2 or 3 R1b,

Krefter said...

Nirj,

By DE it means the subclade couldn't be found, it doesn't mean it's DE*. You could say all the samples had BT if you wanted to.

Alexandros said...

@Aram
Surely makes more sense, but where do you base these conclusions regarding the haplogroups? I am not trying to refute you, but we really need to have some credible data on the Y-hgs soon to avoid this confusion, as we are all trying to run to conclusions, with data not yet entirely confirmed (to clarify I am just talking about Y-hgs, not the autoosmal data)

Aram Palyan said...

This is the regional distribution of R1b among the modern Armenian populations.
https://drive.google.com/file/d/0BwiYFZ1GMcZLWE1iMW02Qk9BUkE/view?usp=sharing

Clearly the highest frequency is in the East. Remembering that Talyshs, north Iranian Gylaks, Iranian Lurs and also Lezgins are also high in R1b so we can have the approximate idea from where Armenian R1b came. It is highly improbable that it moves from Yamna to Balkans crossed all Anatolia and Arm. Highlands and had a founder effect in Eastern Armenia and Iran.

Aram Palyan said...

Alexandros

My data on Y Hg is from this table

http://abload.de/img/nature14507-sf61rwr50.jpg

Alexandros said...

Thanks Aram. Are these supplementary tables from the paper? I still did not have the chance to read the whole paper with all the supplementary material..

Regarding what you mention on the distribution of R1b in the Armenian territory, I have noticed from the Cinnioglu et al paper, that the highest frequency of R1b in Anatolian Turks is in the North Central (area 2), followed by South Central (area 6). What would you make of this regarding the direction of R1b migrations to/from Anatolia?

Mike Thomas said...

To interject- nothing
Given the often times large migrations that have occurred in that region in the last couple hundred years, not to mention the other 3000 since the BA

Aram Palyan said...

Mike
Everything is possible. But such a movement means that R1b came from Balkans to East Armenia/Iran circa 2000 BC just before the establishment of Hittite empire. so generaly this does not change much to the fact that R1b in LBA Armenia has IE origin and not a Hurrian. What some people try to show.

But the most probable route remains from East to West trough north Anatolia.

Mike Thomas said...

Aram

I don't know where R1b came from to Armenia. On the basis of present evidence, it could be east or north. But I am more sure that it wasn't brought by "The Armenians", beuuase such people didn;t exist 3000 BC. IN fact, Im not even sure that R1b was exclusively even PIE at all

Aram Palyan said...

Mike

I don't think I ever said that Armenians existed in 3000 BC.
What I am saying is that in the current stage of our knowledge the R1b in Northern parts of West Asia is most probably a solid marker of IE presence.
If it is not the case. And R1b has no any correlation with IE in Northern West Asia then we can start to make other assumptions and speculations about other Hgs or even non-Steppe origin of PIE.

p.s. In my opinion the R1b is a marker of IE presence in Northern West Asia. If Central Asian origin of this R1b is shown I will change my mind.

Aram Palyan said...

Alexandros
Yes that table is from the paper. The map of R1b frequency is from elsewhere.

My opinion about the movement of R1b is like this. It has a Steppe origin. It's highest frequencies are close to Caspian and Black sea. This mean he was moving by the costline or rivers. So if the origin is the Yamna and not a place like Turkmenistan, then it moved South to Caucasus later moved to Greece trough North Anatolia. The Balkanic route is also possible but it should be early rather than late. Two different routes are also possible but in this case we should find some differences in North Iranian R1b-Z2103 subclades and Greek ones.

Nirjhar007 said...

Aram, we need aDNA from C asia and W Asia before making any comments on Rib origins BTW I do think Armenians existed around 3000 BC their language have some archaic traits...

Mike Thomas said...

Aram

I actually agree with what you're saying. The connecting link is Majkop, via Daghestan..
What I'd like to see is aDNA from the Nth Caucacus and Ukraine. Is it also R1b, or R1a, or both ? But so far, R1b and R1a seem well separated.

Krefter said...

@Anyone,

Is all I need to make use out of the BAM files from Allentoft 2015 is provided by Felix here?

http://www.y-str.org/2014/04/bam-analysis-kit.html

I pretty much just download his program and press a few buttons?

Karl_K said...

Go Krefter! You could have done it by now! It's not hard, it just takes a little time and good download speeds to be the next Felix.

Mike Thomas said...

Krefter,
Ive been wondering the same thing. I hope that's all that's required, but I doubt it for some reason.

Krefter said...

I'm not going to take the risk of damaging my laptop. Is anyone else able to do it? BTW, a Yamnaya and Armenian R1b from Allentoft have been confirmed to be R1b1a2a2. So far Bell Beaker R1b is 2/2 R1b1a2a1a-P312(one is confirmed U152) from Haak and Allentoft.

http://www.anthrogenica.com/showthread.php?4640-Population-genomics-of-Bronze-Age-Eurasia-(Allentoft-et-al-2015)&p=88714&viewfull=1#post88714

Nirjhar007 said...

I think the authors intentionally gave the data this way i think to challenge or to test the Genome blogging community:).....

Karl_K said...

Actually it's pretty simple. And those tools let you do it from a windows computer, which is usually the problem with people less familiar with unix systems. You do have to use the command line and understand if there is an error, but you can just Google all that and have answers in seconds.

I once sat through a class of uninterested bioinformatics students who basically re-assembled their own human genomes on their laptops. And that was several years ago.

Aram Palyan said...

Nirjhar

Yes we need aDNA from South Central Asia. Also from Greece. Greece is also important. I don't think Hittites will be much different from ancient Armenia, so they will not resolve this issue.

BTW an interesting article about this study

http://www.nytimes.com/2015/06/16/science/dna-deciphers-roots-of-modern-europeans.html?hp&action=click&pgtype=Homepage&module=photo-spot-region&region=top-news&WT.nav=top-news&_r=1

Grey said...

to be a cracked record again if part of the R1b expansion was small groups like the African blacksmith guilds but connected to copper working rather than iron then they could potentially move very far relatively fast because they wouldn't have had to fight their way from A to B - just hop from trade node to trade node.

http://en.wikipedia.org/wiki/Blacksmiths_of_western_Africa

if so you might find little clusters of R1b anywhere there was ancient copper

(and if they'd originally come from the southern Urals they might have a cluster of red hair genes also)

Mike Thomas said...

Has anyone discerned the progression of haplgroups in Scandinavia. Ie is there a pattern from LN/EBA to mid Bronze Age ?

AWood said...

From the data and the conclusions from the paper, it looks like the R1b pocket in Armenia is an outlier from the Yamna and European shared "Caucasus" ancestry. This indicates there was an eastern side expansion around the Caspian to Armenian highlands which is independent from any western expansions. I believe another wave of R1b-L23(xL51) is from a western expansion around the Black Sea and settled in southern Balkans (Greece/Albania) and Anatolia. Unfortunately we need more data to support this. In turn I believe Austria-Hungary is the birth place and/or bifurcation of L51+, and we see the remaining western expansions descend from this clade with "Western" IE speakers. We need to see more R1b SNP results to support this claim.

Simon_W said...

Hungary Bronze Age: 0/6 are R1b.

But R1b was present in Corded people, contrary to what many had expected. (Me not included.)

I'd really question the narrative that a wave of R1b people migrated up the Danube to central Europe. This has been so often repeated that many take it for granted.

But we don't need a massive wave of R1b people, because it's all from founder effects. It's quite possible that modern West European R1b was from the R1b minority in Corded people.

Simon_W said...

The relationship of Sintashta with the EEF admixed Corded people is fascinating. By the way, the Russian anthropologist V.V. Bunak has noted long before that the physical type of the Srubna culture differs quite a lot from the earlier Yamnaya and Catacomb people. The Srubna type resembles the modern central Russians and has smaller absolute measurements than the earlier steppe cultures. This is probably a consequence of EEF admixture. And of course, Srubna being dated to 2000 BC - 1500 BC, it's contemporaneous with the adjacent Sintashta culture.

Simon_W said...

I find it strange that they didn't include published EHG genomes in their dataset. Instead they use MA-1 to calculate f3 stats for Yamnaya and then they wonder that the admixture signal for Armenian-like admixture is so weak...

rozenfag said...

@Simon_W :
The paper was sent to Nature on 14 February 2015, before Haak published genomes, so they apparently couldn't compare them at that time.

apostateimpressions said...

Hi everyone, is there a table around that estimates Yamnaya-like admixture in modern European countries like Britain?

Am I correct in thinking that R1b came from the steppes during the BA?

Would R1a and b have been genetically close back in the steppes?

Btw there are newspaper and journal articles on this paper that may be of interest:

http://www.dailymail.co.uk/sciencetech/article-3007954/The-origins-modern-Europeans-DNA-reveals-Yamnaya-people-Russian-grasslands-invaded-central-Europe-4-500-years-ago.html

Thanks

Davidski said...

I'll have all of the samples soon. I'll start running them early next week.

Alberto said...

That's great news, can't wait to see your analysis.

From the data on the paper I've not been able to make much. All the formal stats provided are not too informative. And some genomes seem to be of low quality (the ones from Montenegro and Lithuania, apparently).

I'm most curious about the Sintashta genomes. They seem to be similar to CWC or Unetice, but I think there might be some interesting differences. From the Bronze Age Armenian samples I'm not sure what to think. They seem quite "eastern" (little affinity to both WHG and EEF), but it might be a wrong impression from those limited stats. Soon we'll find out.

Kurti said...

results of RISE416.txt (BaArmenia)

23.69% Gedrosia
0.00% Siberian
0.00% Northwest_African
0.00% Southeast_Asian
33.20% Atlantic_Med
19.53% North_European
0.00% South_Asian
0.00% East_African
0.00% Southwest_Asian
0.00% East_Asian
23.57% Caucasus
0.00% Sub_Saharan


The results are not even remotely "identical" to modern populations of the same region.

I think I know what happened as I was saying the Semite (Assyrian) expansion probably happened.

Matt said...

Looking forward to seeing your analysis David, you have techniques at your disposal this paper doesn't and I'm sure you'll find new stuff.

Examining the D stats in their Supplementary Table 5 (http://www.nature.com/nature/journal/v522/n7555/extref/nature14507-s5.xlsx), just to explore:

For Sintashta

D(Yoruba,Malta;Sintashta,Pop) is positive for most populations. So Sintashta less related to Mal'ta. No significant stat for e.g. D(Yoruba,Malta;Sintashta,Bell Beaker) while D(Yoruba,Malta;Sintashta,Yamnaya) is D = 0.029, significant at Z=8.37.

D(Yoruba,hunterW;Sintashta,Pop) for Bronze Age Armenia is D = -0.039, significant at Z=-12.56 and for Yamnaya D=-0.0107527, Z=-3.54. So both of these indicate that Sintashta is closer to hunter W than either of these two.

Likewise for Neolithic Central European D=-0.0135, significant at Z=-3.54 and Bronze Age Corded Ware actually positive at D=0.0084, Z=2.60. So out of these 4, only Corded Ware is closer to hunterW than Sintashta.

D(Yoruba,neolC;Sintashta,Pop) gives Yamnaya D=-0.013 and Bronze Age Armenia D=-0.0009, so Sintashta is indeed closer to Neolithic Central Europeans than both of these (more marginally for brArmenia). Non-sig for Andronovo.

Seems all more consistent with the idea that at least some admixture into Sintashta came specifically from Bronze Age East-Central Europe and not Bronze Age West Asia (whether it also came from other places or not).

Another minor one - D(Yoruba,Ust-Ishim;Sintashta,Pop), they are all positive, except for Neolithic Hungarians whch is mildly negative at a non-significant level.

Which implies that Sintashta is less related to Ust Ishim than all other populations (including Neolithic Central Europe although those are non-significant) and more "basal Eurasian". Must be wrong somehow.

The Sintashta samples on the ADMIXTURE also show some strange purple African component, even at fairly high K. Not sure why that is.

For Bronze Age Armenians:

Trying to gauge Malta affinity for Bronze Age Armenia with the stat D(Yoruba,Malta;Bronze Age Armenia,Pop), I see the average of the Neolithic Hungarian and Central European populations for this stat is D=-0.0146 and Z=-3.50. So Bronze Age Armenians are closer to Malta than Neolithic Europeans.

At the same time, similar stats for Yamnaya is D=0.048 and Z=12.2, while for Corded Ware is D=0.28, Z=7.41 and Bell Beaker D=0.20 and Z=4.82.

So this implies the Bronze Age Armenia was not very high in Malta affinity, more comparable to Neolithic Europeans than Bronze Age Europeans who are quite a bit closer to Malta than BRArmenian.

To check out Neolithic European farmer affinity for Bronze Age Armenians D(Yoruba,NeolithicHungarian;BronzeAgeArmenian,Pop).

For Yamnaya the stat is D=-0.01378, Z=-5.388, so closer than Yamnaya. While for Andronovo, the stat is D=0.0033, Z=1.28, so more or less Andronovo is as close to Neolithic Hungarians as Bronze Age Armenia. Corded Ware D=0.0106,Z=4.496 and Bell Beaker D=0.172,Z=6.566, so both of these populations are closer to Neolithic Hungarians than Bronze Age Armenians.

Finally hunterW D=0.0131, Z=4.20, so Western European hunter gatherers are closer to Neolithic Hungarians than Bronze Age Armenians are.

(If any of the method above doesn't seem clear, compare - http://www.nature.com/nature/journal/v522/n7555/fig_tab/nature14507_ST1.html, unless I've made any big mistakes here).

Alberto said...

@Kurti

That looks like much less ENF and much more WHG and ANE.

D-stats seemed to show little WHG (SHG in this example) affinity:

Yoruba hunterN hunterW Ust z-core: -37
Yoruba hunterN baBb Ust -23
Yoruba hunterN baYam Ust -21
Yoruba hunterN NeolHu Ust -18
Yoruba hunterN baArm Ust -14

So it seems quite less affinity than Neolithic Hungary. Maybe the high ANE rises the North European?

Matt said...

Kurti, comparing those results with the Armenians on Dodecad K12 does suggest significant change, although obviously SNP overlap, calculator effect, etc.

Re: BaArmenia, looking at the f3 stats, for f3(Ju_hoan_north,Pop,baArm), it's unusual.

You'd Bronze Age Armenian expect them to have high f3 with Lezgins, who are the most similar to them on the the SI ADMIXTURE from Allentoft.

But no. For modern populations, its Scottish, Icelandic, Estonian, Lithuanian. Although Abkhazians and Georgians are relatively high up there as well, as are Corded Ware and Croatians. All with roughly comparable levels of SNPs.

Not much of what we'd expect as a simple regional pattern. And the f3 is pretty low for everyone.

Instead, a pattern a little akin to some of the Bell Beaker David's previous posted f3 stats for, where IIRC there was a dual affinity to both Basques and Lithuanians (which is present, but reduced in the Bell Beaker f3 stat here as well).

Kurti said...

@Matt

The 20% North European is mostly WHG. Thats the weird part. The sample has like 10% ANE and 20% WHG. 4 times! as much WHG as modern populations in the same region.

Also the ENF is Atlantic_Med which points that this can't have come from the Steppes, because those "lacked" Atlantic_Med.

It seems to be the remnant of early farmers.

As said dozen times. It really seems when the Semites (especially Assyrians) expanded they significantly changed the genetic make up of the region, by bringing a Red Sea like component from the Proto Afro_Asian homeland in Egypt. This probably gave birht to "Southwest Asian".

Just look at it, there is no Southwest Asian component!

Roy King said...

@Kurti
If the BA Armenians have no Southwest Asian component, in contrast to modern Armenian, that is surely a major result! It would make sense of the Assyrians brought Levantine and Arabian Peninsula populations into the Armenian area. They did have interactions with the Uratian/Lan Van populations during the acme of their hegemony.

Davidski said...

That's probably based on Genetiker's work.

I'm getting all of the genotype data from the paper tomorrow, so let's wait and see.

Krefter said...

According to Richard Rocca another Bell Beaker has come out R1b-P312+. This time it isn't U152, it's Z196+. Z196 is a widespread and popular subclade of DF27!! If DF27 was already in Germany over 4,000 years ago, that can explain it's widespread distribution today.

Richard Rocca. Anthrogencia.
"German Bell Beaker sample SAMEA3325421 is P312+, but also Z196+, meaning he is also DF27. What is surprising however is that he is also Z195-. I don't think we have any modern Z196+Z195- samples, but I could be wrong. This of course could be huge for R1b!"

Davidski said...

Any word on the R1b of these new Yamnaya samples?

And what about the Sintashta/Andronovo R1a?

Krefter said...

I was wrong, it's another R1b-U152. I spoke too soon.

"Any word on the R1b of these new Yamnaya samples?

And what about the Sintashta/Andronovo R1a?"

Besides Geneticker I haven't heard anything.

Vernon Chastain said...

Where are these R-U152 Beaker samples from, Krefter? Germany?

Davidski said...

See Figure 1. in the post above for sampling locations.

Vernon Chastain said...

Interesting that U152 is 50% (2/4) of the northeastern Alpine EBA samples we have, and is also absent in the Remedello samples. Modern day, U152 is far more common in northwestern Italy than it is northeast of the Alps. Certainly makes me wonder how and when that happened.

Mike Thomas said...

We can exclude old ideas (but still lingering) that R1b expanded from Italy, thats for sure.

Id suspect R1b really made headway in Italy after the Bronze Age, esp Iron Age

Vernon Chastain said...

What do you suggest, Mike? Urnfield expansions; Proto-Villanovan in particular for Italy?

Mike Thomas said...

Id be guessing. But two suggestions:

1) Archaeologically: the Bronze Age was a low population, pastoral -type economy in much of Italy - esp north. Perhaps this is when pastroalist, R1b-bearers entered. The Iron Age saw rapid rise in population = ? consolidation

2)Working backwards, one can collate all the R1b groups from Italy (eg look at ftDNA), and do variance and age-estimations within italy, and compare it to other regions. Admittedly post-Hoc, it can give some clues until we see BA & IA samples from Italy.

Nirjhar007 said...

David, According to Genetiker Andronovo is R1a-z645 the Ancestor of Z-280 and Z-93!!! your comments?

Davidski said...

Andronovo R1a-Z645 can only be ancestral to R1a-Z93, because R1a-Z80 is from Europe.

Nirjhar007 said...

No i mean't the Mutation is Ancestral to both European Z-280 and Asian Z-93, Yes Z-280 is European but Z-93 is also Asian, so we can assume people with such Ancestral mutation lived in Central Asia at least due to the lack of sampling from other parts of Asia...

Roy King said...

The Bronze Age Hungarian (RISE374) who is Haplogroup G is derived for Z6308 which is equivalent to PF3177--the immediate SNP above Oetzi's L91 Y, according to Ted Kandell of Open Genomes Foundation.

Davidski said...

They did live in Asia. But they couldn't have lived in a lot of different places, because Z645 is a young mutation.

Z645 was probably restricted to North/Central/East Europe and the Eurasian steppe until the Late Bronze Age. Thereafter it most likely expanded as Z282 derived lineages in Europe and Z93 in Asia.

I have said this before though.

Nirjhar007 said...

David, Yes but certainly we have to see before we can judge and it will be interesting also to see if R1a-M417 Appears in other parts of Asia or not before the 2000 BC Period, i'm certain it will be there in Indus Valley but we have to wait.

Nirjhar007 said...

i'm suspecting Tarim Mummies may be also Z-645 like the Andronovo ones....

Average Joe said...

Could the high levels of R1b amongst the Yamnaya samples be due to the possibility that R1bs were dominant in the Yamnaya culture while the R1a1s were more of a serf-like group within the culture?

Nirjhar007 said...

Seriously? serf like?:) to keep it simple we are missing samples from the Western parts of Yamnaya where we can assume there will be R1a.

Kurti said...

@Roy King

results of the Iron Age Armenian.

Again no sign of Red Sea/SW

14.62% S-Indian
34.51% Baloch
41.86% Caucasian
5.53% NE-Euro
0.00% SE-Asian
0.91% Siberian
0.00% NE-Asian
0.00% Papuan
2.48% American
0.08% Beringian
0.00% Mediterranean
0.00% SW-Asian
0.00% San
0.00% E-African
0.00% Pygmy
0.00% W-African

Krefter said...

Nirj,
"David, According to Genetiker Andronovo is R1a-z645 the Ancestor of Z-280 and Z-93!!! your comments?"

Geneticker has not posted the clades any of the Allentoft samples are negative for. All we know is the Andronovo R1a is R1a1a1b, nothing says it is R1a1a1b*.

Kurti said...

But what I don't understand how did they even come to think this is "identical" to modern Armenians? This particular result here looks more Iranian than anything and is even slightly more eastern and less Southern(Southwest Asian) shifted than modern Iranians!

Kurti said...

RISE416 sample from Bronze Age Armenia appears even like a mix of Sardinians and Lezgians.

Davidski said...

Average Joe,

It seems more likely that Yamnaya near the Caspian carried almost exclusively R1b.

On the other hand, R1a was found among steppe groups that expanded into their territory from the west towards the end of the Early Bronze Age. Here's a quote from the Allentoft et al. paper.

"From the beginning of 2000 BC, a new class of master artisans known as the Sintashta culture emerged in the Urals, building chariots, breeding and training horses (Fig. 1), and producing sophisticated new weapons. These innovations quickly spread across Europe and into Asia where they appeared to give rise to the Andronovo culture19,20 (Fig. 1)."

https://drive.google.com/file/d/0B9o3EYTdM8lQdzRlWXBQaXlnMGc/view?usp=sharing

It's hard to say what happened to the descendants of the eastern Yamnaya people at this time. Some were probably incorporated into the ranks of these newcomers, while others might have migrated out in a hurry. In any case, what we might be looking at here is a major ass whooping that forced R1b to rush out of the steppe.

Just a thought.

Krefter said...

The single Corded Ware R1b is confirmed to be R1b1a2a-L23, but he is negative for Eastern-branch Z2103 and western PF6543(parallel to L11). Although he wasn't tested for the ancestor of L11: L51. There was a R1b-L23* from Samara Yamanya, and I'm pretty sure it's found in Europe and West Asia today, but I don't know much about it's modern distribution.

Anyways, this Corded Ware R1b is older than any Bell Beaker R1bs. It's from 2880-2630BC, before Bell Beaker was in Germany. So, this is big news for Western European-R1b. It's evidence that Bell Beaker-itself is the not the source of R1b-L11, but that R1b was introduced to Bell Beaker by Eastern European immigrants.

The I2s and G2as continuously coming from EEF-like people(Italy, Hungary, in Allentoft) puts nail on the coffin for the idea R1b-L11 developed way way back in the middle of West Europe.

Kurti said...

Have to correct myself.

RISE416 sample appears roughly like an even mix of Basque and Adygai/Lezgian.

Davidski said...

Krefter,

I agree, I think Northwestern European R1b is mostly from a Corded Ware-derived founder effect.

Kurti,

Please don't jump to any conclusions before we've had a good look at the "certified" genotype data from the study which is on its way.

capra internetensis said...

@Krefter

So you figure Bell Beaker got their R1b from Corded Ware? That would make sense I guess. Maybe their Iberian component had I2.

It looks like the EEFs were not going down without a fight - they seem to have taken Hungary back from the Yamnaya guys in the Bronze Age!

Matt said...

@ Kurti, the 63 Armenians on Dodecad, average:

Gedrosia 16.9
Siberian 0.0
Northwest_African 0.0
Southeast_Asian 0.0
Atlantic_Med 9.6
North_European 3.6
South_Asian 0.2
East_African 0.0
Southwest_Asian 12.5
East_Asian 0.0
Caucasus 57.1
Sub_Saharan 0.0

So compared to the Bronze Age Armenia sample, the differences ancient to modern are:

Gedrosia -6.8
Siberian 0.0
Northwest_African 0.0
Southeast_Asian 0.0
Atlantic_Med -23.6
North_European -15.9
South_Asian 0.2
East_African 0.0
Southwest_Asian 12.5
East_Asian 0.0
Caucasus 33.5
Sub_Saharan 0.0

The Southwest Asian does change as you observe (good observation), but perhaps as or more significant is is a strong dynamic of replacing Atlantic_Med and North_European with Caucasus.

Looking at the f3 stats though, the Bronze Age Armenia isn't really close to early Neolithic Hungarian Farmers at all though:

F3 (Ju_Hoan_North, Test, Neolithic Hungary), a sample of populations low to high (Armenia linked population bold):

Aleut 0.2608298201
Bedouin2 0.2611187231
Yemenite_Jew 0.262430269
Bronze Age Yamnaya 0.2629545154
Bronze Age Armenia 0.2649539300
Bronze Age Sintashta 0.2685953444
Lezgin 0.2682901926
Adygei 0.2689554483
Iraqi_Jew 0.269054765
Abkhasian 0.2699425963
Bronze Age Corded Ware 0.2703419305
North Hunter Gatherer 0.2705927704
Georgian 0.2707205837
Russian 0.271471889
Armenian 0.2715359601
Ashkenazi_Jew 0.2720372777
Finnish 0.2723865444
Iron Age Armenia 0.272394737
Bronze Age Bell Beaker 0.2726386385
Estonian 0.274129126
Western Hunter Gatherer 0.2745377338
Lithuanian 0.2751677542
Czech 0.2756120398
English 0.2758885338
Icelandic 0.2761527209
Croatian 0.2761817359
Bulgarian 0.2762201845
Greek 0.2764158238
French 0.2767582805
Bronze Age Hungary 0.2785406258
Pais_Vasco 0.2788517772
Italian 0.2788529016
Basque 0.2793295167
Sardinian 0.2819075687
Bronze Age Remedello 0.2835522885
Neolithic North 0.2841163197
Neolithic Central 0.2867090951

A population that looks like a mix between Lezgins and Neolithic Europeans, you would expect to have higher f3 with Neolithic Europeans than Lezgins.

But Bronze Age Armenia is less like Neolithic Europeans than Lezgins.

Grey said...

Krefter

"Anyways, this Corded Ware R1b is older than any Bell Beaker R1bs. It's from 2880-2630BC, before Bell Beaker was in Germany. So, this is big news for Western European-R1b. It's evidence that Bell Beaker-itself is the not the source of R1b-L11, but that R1b was introduced to Bell Beaker by Eastern European immigrants."

Or maybe BB developed out of an artisan caste within Corded Ware.

Srkz said...

First diploid genomes:
https://www.dropbox.com/sh/mqp4gxtzpng3kom/AAAYJ7dvojikMCF-q75NRi_Ca?dl=0

RISE71 Gedmatch ID M671253
RISE407 Gedmatch ID M691697
RISE412
RISE413
RISE416

Sintashta RISE386 will be ready soon

Grey said...

@Average Joe

More likely imo that R1a and R1b were originally divided geographically for some bio-region type reason: north-south or east-west or forest steppe vs the other kind etc.

Grey said...

@myself

"Or maybe BB developed out of an artisan caste within Corded Ware."

Or maybe river BB developed that way and maritime BB out of an Iberian version of the same thing.

Aram Palyan said...

Kurti

I think the situation is quite simple.
The R1b came in Armenia circa 3000 BC - 2000 BC
This aDNA are from Syunik (Kapan) which has the highest R1b today 40%

So if You find that they are closer to Iranians then this mean that the most probable source of Armenian R1b is the North Iran. In this case Yamna story also dramatically changes.

On the other hand if they are more Europe shifted (as showed in Alentoft paper) then the source of Armenian R1b is the Steppe.

Why I am so sure that the change is related to the R1b, because the G and J2 in Armenia has a very high TMRCA. Only the R1b is young something like 5000 years.

Alberto said...

@Kurti, Matt

I think that with modern calculators we might be seeing a lot of artefacts because of a not too high coverage genome and because of an unusually high (by modern standards) amounts of ANE. I would wait for David's analysis to have a better understanding of them.

Also, Kurti, it should be safe to consider that these people were recent arrivals to the area, so it doesn't necessarily mean that SW Asian was not present in the area before; rather that these newcomers didn't get it yet.

Soon we'll know, but to me these Armenians look quite "eastern", but not too "northern" (maybe some Lezgin-Tajik type, though too risky to say right now).

Nirjhar007 said...

//a new class of master artisans known as the Sintashta culture emerged in the Urals, building chariots, breeding and training horses (Fig. 1), and producing sophisticated new weapons.//
They obviously came from South i.e. BMAC.

Krefter said...

Thanks Srkz.

RISE71, Denmark 2196-2023 BC. mtDNA H3b, Female no Y DNA.

ANE K7
WHG: 69.56
ENF: 14.43
ANE: 14.85
East African: 1.16

Less ANE and WHG and more ENF than modern Scandinavians. Score is most similar to North Sea in general, and if anything closest to the British isles, North Netherlands and Germany. Very similar to German Bell Beaker and Unetice, and obviously differnt from German Corded Ware(Scandinavian Corded Ware?).

Eurogenes K15.

North Sea: 50.33
Atlantic: 23.06
West Med: 10.77
Baltic: 8.27
West Asian: 4.51
East Euro: 2.59

Looks noisy, but is probably showing relation to North Sea.

Best Oracle:
Orcadian + West_Norwegian + West_Norwegian + West_Norwegian @ 12.967551

Srkz said...

Unlike HAAK 2015, Allentoft101 "diploid" genomes do not have much diploid SNP's (maybe some large BAM's will do)

Alberto said...

@Krefter

"Less ANE and WHG and more ENF than modern Scandinavians."

Was that a typo? 70% WHG is really high, and 15% ENF really low (thought I don't have K7 results to compare, I'm assuming they're similar to K8?).

They don't look very "Yamnaya" to me. Rather very SHG with some Gokhem, no?

Mike Thomas said...

Yes, that Dane looks very SHG

Krefter said...

ANE K7 spreadsheet. The ANE scores are a little higher than in ANE K8, and WHG is much much higher than ENF.

https://docs.google.com/spreadsheets/d/1684wMM_ZJFoxcxJXK0jkVgeGGEVl5Nw3-Moc_IFrlOs/edit#gid=1051326962

Davidski said...

You guys are confusing the K7 with the K8.

The Dane doesn't look very SHG in the K7.

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