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Sunday, December 27, 2015

Next year the Armenian Plateau hypothesis will collapse


It's been a great year for population genetics and paleogenomics, and also for this blog. I churned out a lot of data in 2015 and managed to make a few discoveries that were subsequently confirmed, or at least, backed up by academia. For instance:

- first to show with ancient genomes that the Anglo-Saxons made a significant genetic impact on England. See here. Eventually confirmed here.

- first to show that the southern admixture in the Yamnaya pastoralists of the Early Bronze Age steppe was Georgian-related rather than Armenian-related. See here. Confirmed here.

- first to show that Anatolian Neolithic farmers were very similar to European Neolithic farmers, and lacked Ancient North Eurasian (ANE) ancestry. See here. Confirmed here.

- first to show using ancient DNA and formal statistics that South Asia experienced massive gene flow originating in Late Neolithic/Bronze Age Europe. See here. Backed up with my help here.

The fact that Caucasus hunter-gatherers (CHG) like Kotias are essentially an ideal fit for the southern ancestry in the Yamnaya is a big problem for the Armenian Plateau Indo-European homeland hypothesis. This TreeMix graph shows why.




Basically, it looks like the Kotias-related ancestry in the Yamnaya came from the North Caucasus, rather than any place closer to the Near East than Georgia. Unless, of course, the southern Caucasus was populated by unadmixed CHG right until the 4th Millennium BC, when the hypothetical Proto-Indo-Europeans from the Armenian Plateau set off on their journey to Northern Europe around the Caspian Sea. But let's be honest, that's extremely unlikely.

Indeed, I expect that next year we'll see the first Neolithic and Copper Age samples from Armenia and/or surrounds, and even though they will be in large part CHG, they'll be nowhere near unadmixed. This will essentially kill the Armenian Plateau hypothesis, and thus leave the Kurgan or steppe hypothesis as the only plausible choice.

In any case, 2016 will probably be the year when ancient DNA helps to settle the Indo-European homeland question once and for all. So get ready for more ancient DNA from the steppe, but also, among others, from Mesolithic and Neolithic Iran, Mycenaean Greece and the Maikop Culture of the North Caucasus. I'm also pretty sure that the Varna man with the golden codpiece will make an appearance in a paper about Neolithic and Copper Age Bulgaria. Bring it on!

66 comments:

Nirjhar007 said...

Let me make an announcement :
Next Year The Steppe Theory Falls.
1. Decider aDNA from India and Iran are coming, which will not only show that the theorized migration from Steppe was a myth but the steppe was the receiver of migrations from Northern-Iran, C Asia etc, which shaped both the linguistic and genetic landscape there.
2. The actual teal is yet to be found ,Teal is a part of CHG, but CHG is not equal to Teal.

Davidski said...

The so called teal in Yamnaya is CHG. That's not even worth debating now. Did you even look at the stats from the Jones paper?

As for gene flow from Iran and Central Asia to Eastern Europe during the Early Bronze Age: big effin LOL.

Nirjhar007 said...

David,
No one speculated two dudes from pre-pre historic Georgia or North Caucasus will be representatives of PIE,
Just like ANE can't be ''PIE'' .
Now, what we just need is some sampling from relevant places say Majkop, Say BMAC,Say IVC/SSC ,Say N Iran, Say Jeitun etc etc.....


As for gene flow from Eastern Europe to Iran, Central Asia and South Asia during the Early and Late Bronze Age: big effin LOL.

Davidski said...

Here's a little doodle that you might understand...maybe if you strain enough.

https://drive.google.com/file/d/0B9o3EYTdM8lQWmhKWk14bFhkcjg/view?usp=sharing

Nirjhar007 said...

Mate, i don't need to understand it. Your situation is actually pathetic, please try to be a bit scientific and wait for the aDNA.
As for the conclusions you are making, no serious academic will take it seriously, even some guys here who knows a bit on genetics, ( i will not name them) know what i'm saying.


Coldmountains said...

@Nirjhar

Calm down and stop trolling. Nobody is superior or inferior because of this. Indian R1a and Indic languages are ultimately from the northwest.

Nirjhar007 said...

Its not about Superior or Inferior, its about being sane.
Yes ultimately from NW, but so far there is no reason to think that the source was the Steppes!.
You will understand when samples from before 2000 BC of India and SC Asia comes out.
Even now, its quite obvious ( taking the biased sampling into consideration) that S Asia didn't receive any suggested impact from the steppes.

mickeydodds1 said...

These are very big contributions to science, David.
At the very least you deserve recognition, some sort of award or accolade.

I mean, these are 'untied threads' and mysteries that baffled older generations of ethnographers and anthropologists for years, if not centuries.
Now we can be certain that many of their speculations - which were NOT based on the sound incontrovertible reasoning of genetic genealogy using ancient remains - were just plain wrong.
Nevertheless, right up to be present,their errors and misjudgements, which to be frank were often politically motivated, as unfortunately the stink of politics and chauvinism pervades this subject in the same way that stink pervades an old blanket, are still being repeated verbatim by some.

epoch2013 said...

Dear David,

Yours is a very, very valuable blog. But please resist the temptation to boast that you were first to point out this or that. It is not necessary, you don't need it. Take for instance Svante Paabo, who tried to prove there was no Neanderthal admixture is modern humans, only to find there was. Being right is only fun for the ones that go off on testosterone. Being wrong is far more beautiful, as it rather caters the curious ones. Ask Svante Paabo how nice that feels.

Nirjhar007 said...

Mickey,
We don't have enough samples, even from the steppes.
Yes David deserves veneration , the testings he does are quite accurate and of high standards,
but his conclusions are always cocky and childish mostly.
But even he will have to change his mindset, just wait and see...

alekoche said...

David, thank you for your ground-breaking work. This blog was my favorite throughout the year. Looking forward to new discoveries in 2016, regardless of which theory they ultimately end up supporting.

Krefter said...

@Nirijhar,

You're in denial. No one knew Indo European languages existed till a couple centuries ago, it happened a gazillion years ago, it doesn't inferiorate Indians if they became IE-speakers with little gene flow. For someone to say American culture is from Britain sounds crazy to Americans. And in a lot of ways it is, but so much of America is its own unique thing. In a much more real way everything in India isn't from Steppe IEs. It's a language and other things, but it isn't everything.

Davidski said...

epoch,

Just having a bit of fun after a few holiday beers.

But I'm pretty damn happy that I was right about the Georgian-related ancestry in Yamnaya, even though Broad MIT/Harvard were pushing the Armenian thing.

Krefter said...

@Davidski,

You were mostly right although you got one thing wrong. You thought Teal was a mixture of EEF-like farmers and MA1-like hunter gatherers.

Davidski said...

I think ANE will make a comeback next year, perhaps under a different guise, and it'll turn out that CHG are indeed partly of that stock. But we'll also learn that MA1 wasn't pure ANE.

Kurti said...

@Dave
"
But I'm pretty damn happy that I was right about the Georgian-related ancestry in Yamnaya, even though Broad MIT/Harvard were pushing the Armenian thing. "

Actually Dave you were not the only one who was saying that Armenian like was rather inaccurate. Before you even came to the Georgian conclusion I had my discussions with LeBrok on Eupedia (which anyone can take a look at), that I doubt Armenians are a good source and I assumed the "West Asian" kind ancestry would rather be like a population which is higher in the Gedrosia, portion, simply out of the logic that this "Armenian like "population was described as ANE rich and the more ANE rich populations in West Asia were heavier in Gedrosia (Lezgians, Georgians, Iranians, Kurds, North Caucasians) in comparison. And I took Lezgians as my guess. And tis without any aDNA at hand. Not saying you were wrong in this. Just that many people had the same theory.

And I am quite sure I also argued here any many other places that the Northern Near East could be divided into two genetically seperate components, a Western part which was EEF and an Eastern part which I called "Herders" and I said those herders would be EEF like with ~40% of ANE admixture. Than came CHG which can simply be modeled as ~35% ANE (despite this being shared ancestry rather than real ANE).

There are many other things where I can caim to have been right. I am pretty sure other users too. But there were also other things were I was quite wrong.

@ Nirjhar007

Imo pre Neolithic samples from SOuth_Central Asia will turn out as EHG like, later samples could and will show CHG and maybe even some EEF admixture. Iranian Plateau will also be interesting.

But thats of course just my opinion.

Kurti said...

I also don't think that MA1 is pure "ANE". And I am sure I said this already quite some times.

this MA1 individual will at the end of the day turn out as something
South_Central Asian merged with ancient(pre Han like) Siberian admixture.

Davidski said...

Point is, I didn't just have a theory. I actually demonstrated that it was correct.

http://eurogenes.blogspot.com.au/2015/10/yamnayas-exotic-ancestry-kartvelian.html

Romulus said...

Humble as always David, is that the Australian or the Polish?

Davidski said...

Krefter,

I'm seeing a very consistent signal of admixture in Kotias from a source basal to MA1 and Eastern HG. The levels of the admixture vary quite a bit, probably due to the lack of the right reference population, and perhaps also low quality of MA1, but there's something there related to the so called ANE.

https://drive.google.com/file/d/0B9o3EYTdM8lQcGhSWm5DOHhaN0E/view?usp=sharing

Romulus,

More intelligent contributions, less Medicentric butthurt in 2016. Thanks in advance.

Davidski said...

Here's another one, this time with a slightly bigger edge from the base of MA1/Eastern_HG to Armenians, Georgians and Kotias.

https://drive.google.com/file/d/0B9o3EYTdM8lQRkwxeE11b2c3VTg/view?usp=sharing

All of that stuff about ANE in the Near East in the first half of 2015 wasn't just a coincidence.

Aram said...

The Southern component of Yamna was best fit by populations who have low or inexistant EHG. That's why Iraqi-Jews were a better fit than Armenians. But offcourse Georgians were better because they have lower ENF, and they lack EHG also.

For the extra EHG found in BA_Armenia ( South Caucasus ) my bet is that he started to infiltrate the end of Kur-Arax culture so at Early Bronze Age.
Satsurbia showed that there was no EHG in South Caucasus in Mesolithic and it is unlikely that it appeared with Anatolian and Mesopotamian farmers of Shulaveri Shomu culture .

Davidski said...

Not sure if Georgians lack EHG. They look like they do have some, or at least something related. These D-stats more or less match the last TreeMix graph I linked to above.

Druze Armenian Eastern_HG Chimp -0.0095 -6.994 562741
Iranian_Jew Armenian Eastern_HG Chimp -0.0057 -3.328 562741
Iraqi_Jew Armenian Eastern_HG Chimp -0.0118 -6.304 562741

Druze Georgian Eastern_HG Chimp -0.0152 -9.724 562741
Iranian_Jew Georgian Eastern_HG Chimp -0.0114 -6.035 562741
Iraqi_Jew Georgian Eastern_HG Chimp -0.0175 -8.617 562741

Druze Kotias Eastern_HG Chimp -0.0088 -2.13 484203
Iranian_Jew Kotias Eastern_HG Chimp -0.0043 -1.004 484203
Iraqi_Jew Kotias Eastern_HG Chimp -0.0107 -2.445 484203

Aram said...

In a more relaxed way this PIE homeland quest is like Star War series. :)
A lot off suspense and battles.

In any case even if Steppe theory claims complete victory the role of North Near East will increase as a place for better understanding the IE also as a secondary source of spread zone for some IE groups. This role was substantially underestimated in the Classic Kurgan theory.

Aram said...

Davidski

OK I see. I was referring to the CHG K10 results. But of course now we see that this kind of ADMIXTRUE runs don't tell the whole story where some components can hide in an another component.

I was just wondering how it was that Bedouin_B was showing some EHG in the CHG K10 while more Northern Georgian and Armenian not any.

Aram said...

Davidski

And one more question. If I understand correctly this D Stats Armenians have more EHG than Kotias. Right?

Davidski said...

A direct comparison shows that Armenians and Georgians have about the same amount of EHG-related ancestry as Kotias, which again matches the last TreeMix graph above. Keep in mind though, minor exotic admixture might be skewing things a little in favor of Kotias, who is purely West Eurasian. Bronze Age (BA) Armenians clearly have more EHG stuff than Kotias, even though the Z score is depressed by a smaller SNP count.

Armenian Kotias Eastern_HG Chimp 0.0014 0.327 484203
Armenia_BA Kotias Eastern_HG Chimp 0.0114 2.049 327767
Georgian Kotias Eastern_HG Chimp 0.0069 1.655 484203

But yeah, ADMIXTURE output isn't easy to interpret, and it's also very difficult to nail ancient components. If you cover one angle, you risk messing up other parts of the analysis.

Ryan said...

"I think ANE will make a comeback next year, perhaps under a different guise, and it'll turn out that CHG are indeed partly of that stock. But we'll also learn that MA1 wasn't pure ANE."

I'll go a step further and say the ANE in CHG is more closely related to the ANE in the Northern North America than the ANE in EHG is to that same Amerind ANE. (I hope that phrasing is clear).

I make that claim based off ADMIXTURE runs in the Clovis paper (Rasmussen et al 2014). Take K=11 for example - two "Siberian/Beringian" components show up at low levels in European IE groups - a light pink Aleut/Chukchi component, and a beige Nganasan component. The ratio of the two is pretty much fixed in European IE groups - probably reflecting the initial composition of PIE on the steppe.

What's interesting is that the Aleut:Nganasan ratio for PIE is so high - perhaps as high as 1:3. That's a higher ratio than any group west of the Yukaghir. So my thinking is that something made PIE's ANE heritage much more "eastern" than geography would explain, and I figure CHG would be a good candidate for that.

Thoughts? I suppose I can't exclude the possibility that EHG had oddly eastern affinities (ie that Chukchi and EHG formed a clade and that groups that are geographically intermediate between them now are from some later expansion), or that some third group brought this heritage (maybe with pottery and/or microblades), but CHG seemed a good candidate.




Also re: your, to paraphrase an Australian Prime Minister, only the impotent are pure.

Davidski said...

Really hard to say at the moment without seeing more HG samples from across North Eurasia.

They're probably coming soon.

Kurti said...

Dave said

"Point is, I didn't just have a theory. I actually demonstrated that it was correct."


Point is in many cases I brought the people even close to this kind of theories.

And to "demonstrate" it you need a bit of programming skills and good enough knowledge about aDNA. I am studying computer science and the only thing really holding me back doing these kind of stuff myself is the lust to learn more about aDNA cause I am more interested in archeology/history and there are enough people already doing it.


Anyways you did very good work in that case.



Kurti said...


Dave said

"A direct comparison shows that Armenians and Georgians have about the same amount of EHG-related ancestry as Kotias, "


And here is one of the main reasons why some of your work is screwed percentage wise.

You must be the only one who is actually interpreting shared ancestry between 13-10.000 Kotias and Satsurbila and Eneolithic Samara EHG as "EHG admixture in CHG".

I have been informing you about this since your first CHG calculators came out. That your Eneolithic Samara samples turn out as "pure" 99% EHG while your Kotias sample as ~80% CHG and ~15% EHG. That is completely bollocks dude

Maybe it just feels better for you?

No one else does this not even Jones et al.

Kurti said...

Modern Armenians and Georgians should and have some real EHG which CHG lacks.

But who says that CHG play even a role for Bronze Age admixture in Yamna?

It is quite too old. First when we get the Maykop samples (which I am convinced will be some sort of CHG + some EHG admixture and possibly even EEF) than we will have a better source population. Maybe even the Iranian plateau samples will shows something very interesting.

I even have the feeling the South_Central Asian samples could be of great importance.

Davidski said...

Kurti,

You usually sound like you're high on something. Some examples.

I have been informing you about this since your first CHG calculators came out. That your Eneolithic Samara samples turn out as "pure" 99% EHG while your Kotias sample as ~80% CHG and ~15% EHG. That is completely bollocks dude.

Where did you see that the Samara Eneolithic samples came out 100% EHG in my tests? This is what I got for sample I0122. It looks like 74.6% EHG to me.

Pops Ids Anatolia_Neolithic Caucasus_HG Eastern_HG Western_HG SE_Asian NE_Asian Afro-Eurasian Oceanian
Samara_Eneolithic I0122 0.009261 0.116669 0.74633 0.107088 0.009734 0.00001 0.00001 0.010897

And here it's 69.2% EHG.

Pops Ids SE_Asian Anatolia_Neolithic Caucasus_HG Eastern_HG Afro-Eurasian NE_Asian Sub-Saharan Oceanian SW_Asian Western_HG
Samara_Eneolithic I0122 0.011182 0.00001 0.123402 0.691904 0.00001 0.00001 0.00001 0.014693 0.034708 0.124071

And to "demonstrate" it you need a bit of programming skills and good enough knowledge about aDNA.

WTF are you mumbling about? My TreeMix runs picked out Georgians very deliberately as the non-EHG half of Yamnaya using different methods.

And now we have ancient genomes from Georgia, that Georgians share significant ancestry with, which have been shown to be the ideal proxy for the non-EHG half of Yamnaya.

But who says that CHG play even a role for Bronze Age admixture in Yamna?

Next time you post something stupid like this I'm going to delete it.

Matt said...

Re: Armenian Plateau hypothesis, CHG descendants / cousins unadmixed with Anatolian* ancestry seem pretty likely to have lived in a wide swath of West Eurasia, since they apparently got all the way to India without picking up much or any Anatolian ancestry. So the Yamnaya's CHG ancestors could come from a range of regions.

Armenia seems too close to Anatolia to not have Anatolian ancestry by the time frame Yamnaya begins to form, but I'd have said the same about North Caucasus. It seems kind of strange for the Yamnaya's Near Eastern ancestry to come from a group from the North Caucasus who directly developed pastoralism there, in situ (in the sense of this not having been mentioned before by archaeologists?), then expanded directly from there to directly north, but we will see. It may be that we'll end up with a range of candidate CHG populations who could have contributed to Yamnaya, then the archaeologists will have to sort it out.

*as far as we know Anatolian Neolithic = Anatolian HGs....

Nirjhar007 said...

Matt,
That's what i call a scientific talk, well done.
At the end the real deal is more sampling from relevant places and sampling the untested vital cultures and civilizations both In Asia and Europe, its too early to make any final conclusion, the whole set up will change every time a new aDNA comes!.

Davidski said...

@Matt,

Armenia seems too close to Anatolia to not have Anatolian ancestry by the time frame Yamnaya begins to form, but I'd have said the same about North Caucasus.

Both Satsurblia and the North Caucasus may have been sheltered from Anatolian influences right until the late stages of the Neolithic or even Eneolithic. And after that there may have been more or less unadmixed CHG communities north of the Caucasus near the Black and Caspian Seas.

I'm skeptical that the CHG in Yamnaya can be from anywhere but Satsurblia and surrounds, considering the preference Yamnaya shows for Georgians in TreeMix.

Btw, I don't know how pastoralism spread onto the steppe, but the Khvalynsk people were pastoralists and they knew how to work copper. And yet, at least some of them were almost pure EHG.

So maybe they learnt it? These kinds of things don't need massive invasions to get going every time.

Davidski said...

This is from the second Mathieson et al. preprint at bioRxiv, page 10.

The unusually large cemetery at Khvalynsk contained southern Europeoid and northern Europeoid cranio-facial types, consistent with the possibility that people from the northern and southern steppes mingled and were buried here.

So I'm not sure what the problem is? There's no way the CHG in Khvalynsk and Yamnaya is from further away than the Caucasus foothills.

And that's just the start of Nirjhar's problems. Because Z93 is from much deeper in Europe than that.

Nirjhar007 said...

Pastoralism arrived in E Europe and surrounds from South of Caspian , as observed from the Jarmo related cultures. It reached already there around 6000 BC. But to be fair, it wasn't the only source.
The data don't lie, archaeological data in this case is clear.
Nirjhar has no problem, just that he knows eventually it will be seen, that the Source of Z-93 ( Which can't be from deeper Europe ) and also M-417, was Asia.

Davidski said...

Nirjhar has no problem, just that he knows eventually it will be seen, that the Source of Z-93 ( Which can't be from deeper Europe ) and also M-417, was Asia.

Fraid not, because the area north of the Black Sea is definitely considered Europe.

Grey said...

From my reading the thing about metal working is after the early stages (cold hammering) it needs a lot of wood.

Which makes me think that a population in a region with lots of copper and lots of wood wouldn't have a motive to move to a region with lots of copper but little wood.

However a population from a region with lots of copper lying around on the surface but limited wood and who had hit a metallurgical wall because of it would have a lot of incentive to spread out looking for regions with both.

Shaikorth said...

Ryan, I think there's already evidence suggesting Nganasan component is too young to be relevant in European genetic history and the ANE in EHG and Chukchis/Aleuts is similar.

Figure S1 in "The complex admixture history and recent southern origins of Siberian populations":
http://www.biorxiv.org/content/biorxiv/suppl/2015/04/30/018770.DC1/018770-1.pdf

At K=3 the Nganasans appear a mix of Chukchi/Naukan and Han, which suggests they are a composite containing later East Eurasian ancestry from the south, and have lower ANE affinity than Chukchis. Further this later ancestry is specific to the Siberian region because not even the North Russians show this "Han" at K=3, only Chukchi/Naukan. This implies that when they get Nganasan (and later Khanty at higher K's), it's due to shared ancestry, and Nganasan-like populations are not a source of ancestry beyond their own neighbourhood. The ANE in North and Central Siberia would predate the additional southeastern admixture.

The ethnogenesis of Nganasans, and probably most modern North/Central Siberians, postdates PIE so if their modal component appears in EHG or steppe groups on top of amerindian, aleut etc. it's just a sign of ADMIXTURE not handling drifted populations and ancient genomes well. A comparable event was one of the Lazaridis runs which had MA-1 showing a purely Kalash-specific component and no generic S-C Asian component at highest K's.

Nirjhar007 said...

David,
Z-93 can't be from deeper Europe, its not possible that it came from C-N Europe, the source was C Asia.
BTW you said ''So get ready for more ancient DNA from the steppe''.
Can you tell which sites they include?. Do they have Abasevo etc?.
Of course more testings from CWC,Yamnaya etc are always welcome.

Davidski said...

Nirjhar,

Lots of samples are being tested, including Fatyanovo. Probably Abashevo as well.

You know how they'll turn out, right? All basically Northeast Euro with nothing Central or South Asian, but some with basal Z93 that will turn out ancestral to Indian Z93.

Nirjhar007 said...

Oh ok, thanks for the info. But i think after some Eneolithic-Copper age samples from the Asian cultures and civilizations, that i mentioned earlier , you and other dudes will get the answer on R1a-M417-Z93 and also R1b.



Kurti said...

@Dave

"You usually sound like you're high on something. Some examples."
Your Samara Eneolithic sample is shown as ~10% WHG and ~10% CHG. While Jones et al. shows Samara Eneolithic as ~20% CHG.

Sme of your percentages are screwed because some UHG like ancestry is getting eaten up as "WHG" this is why your calculator shows "extra WHG" in all samples even Sintashta who is around ~40% EEF.

And once again not I am on drugs, you can wiggle and turn it all day long, there is no EHG ancestry in CHG that there is no logic behind this. 12.000 BC samples unlikely have EHG admixture.

Kurti said...

"Next time you post something stupid like this I'm going to delete it."

Mate it seems you are on your aggressive days again. It's quite interesting how you always act this "crazy" on your own blog. If you want to argue with me let's take it to neutral ground cause obviously when you don't have much arguments or someone has a different opinion as yours, you start to shout and threaten.

Now read my post again and not just only this one sentence. Any one with a tiny intellect would understand the meaning behind it.

Georgians have significant percentage of CHG ancestry (~63%) but they also have significantly other ancestry (especially EEF). And even them should not be representative for the ancestry in Yamna.


And thats it of me for now.

Anyone who has the desire to discuss this things I can recommend Eupedia.com There are many people as me who are interested in this field. As far as I know David is also a member there.

Davidski said...

@Kurti,

Jones et al. didn't have the Samara Eneolithic samples because they were published almost a month after their paper.

You're confusing Samara HG with Samara Eneolithic.

Samara HG should always be 100% EHG because that's what formal tests show in Haak et al. and Mathieson et al. This is also what my ADMIXTURE tests show, which means they're correct, at least in this instance.

If the Jones paper shows Samara HG to be 20% CHG, as you claim, then this is not correct, because it doesn't correlate with the formal tests. But that's OK and not particularly important, because ADMIXTURE is not a formal mixture test, and never used in modern major papers to estimate mixture proportions.

The reason I run ADMIXTURE is to design tests for personal genomics customers, and I try to get as close as I can to reality, so I'm actually very happy that Samara HG comes out 100% EHG and 0% CHG in my tests.

For analyses of ancient data that I post on this blog I use methods based on formal stats, like D-stats and TreeMix.

Now, if you get confused about something again I'll just delete your posts. I don't have time to set you straight every time you get confused, because it happens a lot. So think more carefully before you post here again.

Davidski said...

Georgians have significant percentage of CHG ancestry (~63%) but they also have significantly other ancestry (especially EEF). And even them should not be representative for the ancestry in Yamna.

No shit Sherlock.

But I demonstrated that they were the best choice for Yamnaya before CHG from Georgia were available.

CHG from Georgia are easily first, Georgians are second. Not very surprising when you think about it.

Are you able to correctly interpret this graph, or is it too much for you?

http://4.bp.blogspot.com/-KeseDAuCy7Y/Vn_jpuIBQaI/AAAAAAAAD2Y/-Yqed6n86Ig/s1600/Kotias_%2526_Yamnaya_TreeMix.png

Helgenes50 said...

David,

Your next calculator expected for january will be close to your CHG K10

https://docs.google.com/spreadsheets/d/1Gn0Bea98xDJewbBmh1Yua7J6KH9uPAwrGNQqpwmHvtA/edit#gid=636121149

Davidski said...

Yeah, similar, but this new one's better.

Simon_W said...

Schiffels et al. demonstrated with the help of rare variants about 30% Anglo-Saxon ancestry in eastern England and lower percentages in the rest of Britain - thus the British and the English are genetically still more Celtic than Germanic, to put this a little into perspective.
Interestingly, with the MDLP K13 Ultimate calculator Hinx 2 is, among modern populations, closest to North Germans and Swedes, and Hinx 4 closest to the English. (While with your Eurogenes K15 Hinx 2 was closest to Argyll and Hinx 4 to the Irish, thus both shifted westwards.)

Simon_W said...

But I think your argument with the lack of Anatolian farmer ancestry in Yamnaya & co. against the Armenian plateau hypothesis looks solid! Even if the Mycenaeans had low EHG (we'll see) this wouldn't overcome the power of your argument.

Simon_W said...

Considering the 10.6% EHG in BA Armenians (according to the CHG K10 run), the Mycenaeans would have had some EHG even if their ancestors had taken the southern route around the Black sea.

Arch Hades said...

Is there really such thing as a Southern Europoid and Northern Europoid craniofacial type? At least on an idividual basis? I mean there are of course metrical averages for two distinctive groups but there is lots of overlap on individual basis.

Arch Hades said...

I expect the Mycenaeans to be similar to the BA Armenians and have inflated levels of CHG.

Rob said...
This comment has been removed by the author.
Matt said...

OT, but new ancient genomes from Ireland:

http://www.pnas.org/content/early/2015/12/22/1518445113

"Modern Europe has been shaped by two episodes in prehistory, the advent of agriculture and later metallurgy. These innovations brought not only massive cultural change but also, in certain parts of the continent, a change in genetic structure. The manner in which these transitions affected the islands of Ireland and Britain on the northwestern edge of the continent remains the subject of debate. The first ancient whole genomes from Ireland, including two at high coverage, demonstrate that large-scale genetic shifts accompanied both transitions. We also observe a strong signal of continuity between modern day Irish populations and the Bronze Age individuals, one of whom is a carrier for the C282Y hemochromatosis mutation, which has its highest frequencies in Ireland today."

Krefter said...

Ireland was repopulated by R1b-L21, Lactose Tolerant, people in circa 2000 BC.

Neolithic and Bronze Age migration to Ireland and establishment of the insular Atlantic.
http://www.pnas.org/content/early/2015/12/22/1518445113

The fact is R1b-L21 arrived with Steppe ancestry. No more debating where R1b-L21 comes from.

Matt said...

Few cool bits from this paper:

Along with other MNs, Ballynahatty displays increased levels of hunter–gatherer introgression compared with earlier farming populations. D statistics revealed that, out of the three Mesolithic hunter–gatherer groupings from Haak et al. (9), eastern hunter–gatherer (EHG), Scandinavian hunter–gatherer (SHG), and western hunter–gatherer (WHG), Ballynahatty shares the most alleles with WHG and furthermore has the strongest preference for WHG over EHG and SHG out of all contemporaneous Neolithic individuals so far sampled. However, Ballynahatty forms a clade with other MN genomes to the exclusion of WHG and, symmetrically, WHG genomes form a clade to the exclusion of Ballynahatty. Of the three WHG individuals, Ballynahatty appeared to share the least amount of affinity with LaBrana (Spain) and the largest amount of affinity with Loschbour (Luxembourg). To gauge the proportion of Ballynahatty’s ancestry derived from WHG, we used the f4 ratio, f4(Mbuti, Loschbour; Ballynahatty, Dai)/f4(Mbuti, Loschbour; KO1, Dai) (29), to estimate a hunter–gatherer component of 42 ± 2% within a predominantly early farmer genome. Thus, we deduce migration has a primary role in Irish agricultural origins.

(Seems the Ballynahatty MN farmer may have had the highest WHG ancestry out of the other MN we have, although she does not look unusual in the paper's ADMIXTURE or PCA).

These analyses, taken with the PCA and ADMIXTURE results, indicate that the Irish Bronze Age is composed of a mixture of European MN and introgressing Steppe ancestry (9, 10). To estimate the proportion of Yamnaya to MN ancestry in each Irish Bronze Age sample, we took three approaches.

First, from ADMIXTURE analysis (Fig. 1), we examined the green Caucasus ancestry component. We presume an ultimate source of this as the Yamnaya where it features at a proportion of 40% of their total ancestry. In our three Irish Bronze Age samples, it is present at levels between 6–13%, which, when scaled up to include the remaining 60% of Yamnaya ancestry, imply a total of 14–33% Yamnaya ancestry and therefore 67–86% MN in the Irish Bronze Age.

Second, for each Bronze Age Irish individual, we calculated the proportion of MN ancestry by using the ratio f4(Mbuti, Ballynahatty; X, Dai)/f4(Mbuti, Ballynahatty; Gok2, Dai), which gave estimates between 72 ± 4% to 74 ± 5%, implying again a substantial Yamnaya remainder.

Third, we followed the methods described in Haak et al. (9), which use a collection of outgroup populations, to estimate the mixture proportions of three different sources, Linearbandkeramik (Early Neolithic; 35 ± 6%), Loschbour (WHG; 26 ± 12%), and Yamnaya (39 ± 8%), in the total Irish Bronze Age group. These three approaches give an overlapping estimate of approx 32% Yamnaya ancestry


(of course, MN ancestry in Rathlin samples is probably only partially from Irish MN like Ballynahatty).

The high coverage of both Ballynahatty and Rathlin1 allows a sensitive test of haplotype donation to modern populations, with interesting and contrasting results.

Whereas Ballynahatty shows closest affinity with the southwest Mediterranean, Rathlin1 has highest sharing with the geographically closest modern populations, a trend not seen with the other high coverage ancient genome samples. This affinity with Irish, Scottish, and Welsh (a weaker signal from modern English populations is undoubtedly due to the effects of Anglo-Saxon migrations; ref. 36) suggests a degree of continuity stretching over 4,000 y at the insular Celtic edge of Europe

Mark Maz said...

Krefter said...

" No more debating where R1b-L21 comes from."

Yes, south-western Beaker BA Europe. Everything published this year strongly suggests that and not the wishful bullshit you keep spinning here. Enough already. One thing we can finally see in better light is the impact of CW on north central Europe (population wise).

Rob said...

@ Mark

What is the line of evidence supporting your position ?

Krefter said...

@Mark Maz,

I won't get angry because this is just an online thing. We have a Copper and Bronze age Spanish and they have little or no Steppe ancestry. The Bronze age Irish are essentially identical to Bronze age Germans, who shared R1b-P312 with them, while Copper age Spanish lacked R1b-P312.

There's no way around this. They came from Central Europe. I am so tired of some lone posters accusing people who support the obvious(Central/Eastern origins of R1b, massive migration from the Central/East) of being stupid, raciest, and "wishful thinkers". I have no stake in this, I'm on the lower end for "Steppe" blood, etc. Of course everyone into this stuff cares about their own background, but that's not so much the case for me anymore. I'd enjoy learning about Chinese genetics.

jv said...
This comment has been removed by the author.
jv said...

I'm wondering if my ancient grandmother came up through the Caucasus to the Steppes OR if she migrated west from the East Asian Steppes. H6 is on one of the oldest subclades of H. Pre-LGM. My line expanded from the Yamnaya Culture and entered Western Europe with the Corded Ware Culture( clearly a migration) My Haplogroup " shows a long time separation with Central Asian H6) So perhaps my MtDNA remained in the Caucasus or the Iranian Plateau and entered the Steppes via the Maykop Culture. I've read that the Maykop Culture didn't exchange riches, precious metals and gems with Steppe Hunter Gatheres, but perhaps they provided some women. My line H6a1 has been found in Yamnaya Culture Kurgans and associated with Rb1. Eupedia reports H6 is associated with R1a yet the samples tested show R1b. Interesting. jv

Ryan said...

@Shaikorth - Yah, I realize it's not actually the Nganasans - I'm just referring to the component that peaks with them. And yah, I realize East Asian admixture is throwing a wrench into everything.

@Davidski - Might be possible to figure out even without new samples with Treemix and the right selection of populations.

Shaikorth said...

The Nganasan component is pretty much tied to their recent drift and to a lesser degree to that of genetically close populations such as Evens, same way as the Kalash component tends to work. If they weren't so inbred and drifted that wouldn't form and ADMIXTURE would just show more Chukchi/Naukan type of Siberian in ancients and Europe just like happens at K=3 in that run I linked.