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Sunday, March 15, 2015

Modeling Yamnaya with qpAdm


I've been playing around with the new qpAdm program and the Haak et al. dataset over the past few days and managed to come up with what I think are some very promising results. For instance, the Yamnaya genomes from the Samara Valley and surrounds fit rather well as 0.514 Samara hunter-gatherer + 0.486 Georgian (std. errors 0.032, chisq 3.890).

This is an interesting outcome, mainly because Georgian is a Kartvelian language, and linguistics data suggest that the early Indo-Europeans - presumably the Yamnaya nomads or their ancestors - were in close contact with Proto-Kartvelian speakers. Moreover, even though the Yamnaya males tested to date all belong to Y-chromosome haplogroup R1b, which they probably inherited from their hunter-gatherer ancestors, because the Samara forager also belonged to this haplogroup, some of their mtDNA lineages appear to be derived from the Caucasus and/or nearby areas of the Near East.

However, the main problem with this analysis is that it's attempting to model an ancient population as a mixture of a modern one. Indeed, my estimate is that present-day Georgians harbor around 20% of the so called Ancient North Eurasian (ANE) component, which probably arrived in the Caucasus from the Eurasian steppe (see here). If so, then the qpAdm run might be overestimating the non-steppe admixture in the Yamnaya genomes by at least 10%. Nevertheless, I'm quite happy with this result as I await ancient DNA from the Caucasus and Near East.

By the way, I also pretty much nailed the Corded Ware sample: 0.73 Yamnaya + 0.27 Esperstedt_MN (std. errors 0.060, chisq 2.621). Admittedly, an identical result for the same genomes was reported months ago at the ASHG 2014 conference (see here), but that's OK, because it means I'm on the right track.

qpAdm is easy to run, but the quality of its output heavily reliant on the outgroup or "right set" of populations picked by the user. As far as I can see, the following ten populations (a subset of the "magic set" of 15 from Haak et al.) produce the most robust outcomes when analyses are limited to West Eurasian groups.

Biaka
Bougainville
Chukchi
Eskimo
Han
Ju_hoan_North
Karitiana
Mbuti
Ulchi
Yoruba


Why do they work so well? I really have no idea, but through simple trial and error I found that some of the others from the "magic set", in particular the Ami, produced much poorer results.

I'll probably end up posting a whole catalog of qpAdm output in the comments section below over the next couple of weeks. I'm open to suggestions about the models to test and how to improve my runs.

Citation...

Haak et al., Massive migration from the steppe was a source for Indo-European languages in Europe, Nature, Advance online publication, doi:10.1038/nature14317

See also...

qpAdm tour of Iran

Yamnaya's exotic ancestry: The Kartvelian connection

215 comments:

1 – 200 of 215   Newer›   Newest»
Tone said...

Georgian as a close proxy, eh?

I'm really curious to see who the Maykop people were and how they relate to Yamnaya.

Davidski said...

Yes, me too after this.

Mike Thomas said...

That's Patterson's next project, right ?

Nirjhar007 said...

'' linguistics data suggest that the early Indo-Europeans - presumably the Yamnaya nomads or their ancestors - were in close contact with Proto-Kartvelian speakers.''
I find none of the above statements emerging from practical world....

Davidski said...

Mike,

I'm not sure what's happening with that. I've heard they're working on other stuff at the moment, with much older samples. But I don't know the details.

Keep in mind that even if they can get Maikop material, and I don't think they have yet, it might be too degraded to offer anything of value.

Shaikorth said...

What kind of issues Taiwanese aborigines cause as outgroups in qpAdm?

Davidski said...

I don't know what the issue is, or even if there really is an issue? But every time I included the Ami and Dai in the "right set" group the results looked worse, and sometimes much worse. So I dropped them.

Mike Thomas said...

Davidski
Where can one learn to use your K15 calculator using population data ?

spagetiMeatball said...

David, in your new spreadsheet jordanians, armenians, iraqi jews, show pretty significant, between 10 and 20 percent, pre-yamnaya, which seems to be the main neolithic component in europe. Whereas iranians and georgians have much less of this component. Any clues to the significance of this?

Davidski said...

Mike,

I'll run a few Macedonians with the K15 tonight.

sM,

I suspect that the Near Eastern component carried by the Georgians and Iranians is more basal (ie. it has a higher ratio of the so called Basal Eurasian component and a lower ratio of WHG-related admixture) than that carried by populations closer to the Mediterranean. Moreover, it appears that the Yamnaya have mostly this more basal type of Near Eastern ancestry.

Davidski said...

Actually, no, it appears the Yamnaya have a higher ratio of this more basal type of Near Eastern ancestry than early European farmers of western and central Europe.

Alberto said...

"However, the main problem with this analysis is that it's attempting to model an ancient population as a mixture of a modern one. Indeed, my estimate is that present-day Georgians harbor around 20% of the so called Ancient North Eurasian (ANE) component, which probably arrived in the Caucasus from the Eurasian steppe"

But David, there is something that doesn't match. The Georgian-like population that entered the steppe, if anything, had much higher ANE than modern Georgians. Samara_HG had some 37.5% ANE, and Yamnaya about 35% ANE (and this is with the best case scenario for EHG, since ANE is defined as the EHG type, not the type the other population had).

Why do you want to explain any ANE coming from the steppe? Available data does not back up this scenario.

Davidski said...

Alberto,

The steppe is a big place and we don't know who lived east of the Urals during the Neolithic and early metal ages. Maybe pure or almost pure ANE groups were still there at that time and some of them migrated to west Asia and the Caucasus? Just speculation, but maybe they were the ancestors of the Maikop people and Hurrians?

Shaikorth said...

Can you try fitting Yamnaya as Georgian+EHG+Pashtun/Kalash?

Alberto said...

Yes, ok, let's say Kazakhstan could be an origin of this high ANE and low WHG population. But then probably Uzbekistan, Kyrgyzstan and Tajikistan were similar. Turkmenistan and North East Iran could be mixed with ENF.

The thing is that the population that arrived to Yamnaya had a good amount of ENF. So from Kazakhstan they should have gone south, turn west around the south Caspian sea and move to the Caucasus, and from then again up to Samara.

Strange route when Kazakhstan is already much near to Samara going directly.

And besides, that would become basically the same theory I'm proposing, only that you prefer to start the movement in Kazakhstan (which wasn't that Neolithic around 4000 BCE) instead of further south. So what's the advantage about it?

Davidski said...

Shaikorth,

No, I can't, and the output is very definite about that.

Yamnaya as EHG/Georgian/Kalash

0.490 0.532 -0.023 infeasible

Yamnaya as EHG/Georgian/Pathan

0.491 0.539 -0.030 infeasible

Shaikorth said...

That probably implies there was no extra S-C Asian in yamnaya beyond that they share with Caucasus and EHG.

The populations in Central Asia should've been quite different then, though, so it might be worth trying a EHG+Georgian+MA1 fit. If that fails too, the EHG+Causasus model is the one to stick with.

Mike Thomas said...

@ David

Thanks !

@ Alberto

I posted re; references on Cernadova back on the other page.

Nirjhar007 said...

@Alberto
But instead of Kazakh area Maykop as per archaeological data had strong ties with Iran and SC Asia, what about that?

Mike Thomas said...

"Strong " is a strong word. In toto, Majkop appears very original. yet something sparked it all off. There is some growing evidence for central asia/ Iran being a factor. But it might have more to do with the decline of the Balkan copper industry.

Nirjhar007 said...

@Mike
For example the foreign elements of Maykop were none but of Indian and Iranian Tradition + we have the S Asian type ancestry constantly appearing in Yamnaya+CWC! isn't that ''strong'' type indication for movements?
Anyway a comprehensive article is coming soon which will make it a more scientific thought....

Davidski said...

Shaikorth,

EHG+Georgian+MA1 doesn't work.


Mike,

K15 results for several Macedonians.

https://docs.google.com/spreadsheets/d/1SMZ9ZyWM7ITQ3zwXOrimW5uD2I5o4JyPMAVfFjk0EOg/edit?usp=sharing

Grey said...

So if the Atlantic bio-region was particularly suited to cattle *and* crucially if at the same time it was also poorly suited to neolithic crops then those handful of individuals who by fluke were LP might have expanded dramatically when they reached the Atlantic region?

Grey said...

@Alberto

"The thing is that the population that arrived to Yamnaya had a good amount of ENF. So from Kazakhstan they should have gone south, turn west around the south Caspian sea and move to the Caucasus, and from then again up to Samara."

Unless ENF came from there.

Alberto said...

@Grey

"Unless ENF came from there."

You mean if ENF was already in Kazakhstan and these people went directly to Samara?

Then yes, sure, but if ENF was in Kazakhstan it would be because it came from the south, and not much earlier.

Kazakhstan is a good place to look at, and probably a part of the whole thing. But it cannot sustain on its own. It needs connections further south.

Davidski said...

Very interesting read...

"It appears that two young women of 14-17 and 20 years old were born somewhere near the coastlines of the Caspian or Black Seas (North Caucasus region) and later married and moved to the steppe."

The Steppe and the Caucasus During the Bronze Age: Mutual Relationships and Mutual Enrichments

Matt said...

@ David, do the synthetic ANE from K8 (https://drive.google.com/file/d/0B9o3EYTdM8lQSTZualZUSXU5dkE/edit?usp=sharing) have any compatibility with qbAdm?

If so, EHG+Georgian+SynthANE might we at least worth a try or BedouinB+EHG+SynthANE.

Mike Thomas said...

@ Alberto / Grey/ Davidski

Southern Kazakhstan and the Amu Daryu region is most plausible. I'd struggle to see ENF having existed in the Ob-Irtysh or foothils of the Urals that early

Davidski said...

And which uniparental markers would you associate with the migration from this region to the Caucasus and Eastern Europe?

Krefter said...

BTW, anyone who agrees with the ANE/ENF/WHG model can't deny recent Middle Eastern ancestry in Europe. Admixtures and PCAs back this idea up.

I don't care if archaeology and history don't support this idea, somehow(if these DNA tests are accurate) it happened.

In ANE K8 Portugese can fit pretty nicely as 75% Basque and 25% Cypriot.

Davidski, have you ever tried testing the theory of recent Middle Eastern ancestry with formal tests?

Davidski said...

Krefter,

Yes, of course there is post-Neolithic West Asian ancestry in Europe, but it's limited to southern Europe, and only really important in southeastern Europe.

Note that in the K6 the Middle Eastern component is seen in Stuttgart and NE1 at fairly significant levels. So what may seem like recent Middle Eastern ancestry might just be substructure carried over from the Neolithic.

Grey said...

"And which uniparental markers would you associate with the migration from this region to the Caucasus and Eastern Europe?"

The main farmer ydna seems to be fixed at E1, G and some at least of the Js.

So if E1 (plus maybe one of the Js) was fixed to the Levant then G (plus maybe one of the Js) would still have to be the other.

So if the second stream started further east then it's still basically the same story except instead of starting in the near east it starts further east with a rapid Bantu type expansion of foot herders into India, Iran, Near east, Middle east and Europe.

(possibly also moving onto the steppe around the Caspian but getting repulsed cos horses)

Grey said...

@Krefter

"In ANE K8 Portugese can fit pretty nicely as 75% Basque and 25% Cypriot."

That's kind of what I mean.

E1b+J type farmers taking a maritime route out of the Levant via Cyprus and among other things providing the genesis for Atlantic Megalith in Portugal and then a second more overland G+J stream (even though they eventually merged most places).

I'm also wondering if the G+J stream started further east (even if it took the same route after that) as them coming onto the steppe around the Caspian and then retreating (cos horses) might answer the Kartvel language question with IE.

capra internetensis said...

@Grey

Never mind horses, there is also a gigantic forbidding desert in the way.

postneo said...

@alberto

"I'm not proposing a very specific location other than Central Asia, basically because of the lack of data. That area in Turkmenistan seems to show an early and quite developed Neolithic civilization, and it's one of the few sites excavated. But I'm open to better suggestions."

I think its the best bet. It also has to be an area neighboring Yamnaya. We don't have to imagine them as a homogenous population but separate ones from both siberia as well as areas south of turkmenistan that aggregate near Yamnaya.

I have not sees a single map of EHG distribution.

Mike Thomas said...

David

"And which uniparental markers would you associate with the migration from this region to the Caucasus and Eastern Europe?"

I'm not arguing there was definitely a migration ex- Central Asia. But we all know some mtDNA groups have been identified (the "farmer wives" you suggest). From a Y perspective- it'd have to be M269, if at all. Maybe the those immigrant Y groups didn't survive; without invoking genocidal scenarios at the hands of local foragers . Y lines can be very labile and susceptible to extinctions or massive sweeps .

Chad Rohlfsen said...

Here's a couple aqAdm results for Loschbour. I've sent them to Nick Patterson, for review. This is way over my head for interpretation.

Samara_HG 0.833 -1.510 0.162
LaBrana1 0.062 0.218 1.717
BedouinB -1.518 -0.820 0.159


best coefficients: 0.124 0.774 0.101
ssres:
-0.000251376 0.000262097 0.000073354 0.000050382 0.000115783 -0.000113889 0.000164405 -0.000141080
-1.540153729 1.605838849 0.449431381 0.308685189 0.709389903 -0.697784398 1.007293557 -0.864381605

Jackknife mean: 0.130267277 0.760702819 0.109029903
std. errors: 0.087 0.159 0.089


MA1 1.532 -0.780 0.212
Kostenki14 -0.808 -1.473 0.420
LaBrana1 0.009 0.471 1.667


best coefficients: 0.111 0.245 0.644
ssres:
0.000022874 0.000012763 -0.000088375 -0.000018949 0.000105483 -0.000023778 0.000030163 -0.000263358
0.214691848 0.119790104 -0.829459395 -0.177849148 0.990037060 -0.223170340 0.283101017 -2.471800956

Jackknife mean: 0.111001990 0.243926127 0.645071883
std. errors: 0.058 0.159 0.196

Chad Rohlfsen said...

result: LaBrana1 Loschbour Motala_HG Ust_Ishim -0.0368 -4.974 12621 13584 324319
result: LaBrana1 Loschbour Motala_HG Chimp -0.0371 -5.740 13378 14408 324978
result: LaBrana1 Loschbour SwedenSkoglund_NHG Ust_Ishim -0.0405 -4.640 11843 12843 304017
result: LaBrana1 Loschbour SwedenSkoglund_NHG Chimp -0.0385 -4.953 12529 13532 304630

Chad Rohlfsen said...

KO1 is even further from LaBrana than Loschbour.Much more affinity to West Asians too.

result: LaBrana1 HungaryGamba_HG LBK_EN_NE Ust_Ishim -0.0310 -4.228 9098 9680 229751
result: LaBrana1 HungaryGamba_HG Yamnaya Ust_Ishim -0.0284 -3.944 9130 9664 229490
result: LaBrana1 HungaryGamba_HG Yamnaya Chimp -0.0227 -3.255 9776 10231 229983
result: LaBrana1 HungaryGamba_HG Motala_HG Ust_Ishim -0.0435 -5.627 9073 9898 226174
result: LaBrana1 HungaryGamba_HG Motala_HG Chimp -0.0385 -5.348 9650 10421 226662
result: LaBrana1 HungaryGamba_HG SwedenSkoglund_NHG Ust_Ishim -0.0426 -4.637 8552 9313 212180
result: LaBrana1 HungaryGamba_HG SwedenSkoglund_NHG Chimp -0.0362 -4.130 9115 9800 212638
result: LaBrana1 HungaryGamba_HG Iranian Ust_Ishim -0.0235 -3.618 9103 9541 230134
result: LaBrana1 HungaryGamba_HG Iranian Chimp -0.0179 -2.768 9722 10076 230628
result: LaBrana1 HungaryGamba_HG Lezgin Ust_Ishim -0.0263 -3.871 9124 9617 230134
result: LaBrana1 HungaryGamba_HG Lezgin Chimp -0.0206 -3.153 9770 10181 230628
result: LaBrana1 HungaryGamba_HG HungaryGamba_EN Ust_Ishim -0.0378 -4.158 7234 7802 184671
result: LaBrana1 HungaryGamba_HG Finnish Ust_Ishim -0.0275 -3.992 9179 9697 230134
result: LaBrana1 HungaryGamba_HG Finnish Chimp -0.0218 -3.314 9858 10298 230628
result: LaBrana1 HungaryGamba_HG Icelandic Ust_Ishim -0.0321 -4.766 9167 9775 230134
result: LaBrana1 HungaryGamba_HG Icelandic Chimp -0.0261 -3.996 9826 10353 230628
result: LaBrana1 HungaryGamba_HG French Ust_Ishim -0.0294 -4.481 9191 9747 230134
result: LaBrana1 HungaryGamba_HG French Chimp -0.0236 -3.667 9825 10299 230628
result: LaBrana1 HungaryGamba_HG Sardinian Ust_Ishim -0.0262 -3.978 9216 9711 230134
result: LaBrana1 HungaryGamba_HG Sardinian Chimp -0.0206 -3.178 9842 10255 230628
result: LaBrana1 HungaryGamba_HG Chuvash Ust_Ishim -0.0273 -4.038 9110 9621 230134
result: LaBrana1 HungaryGamba_HG Chuvash Chimp -0.0215 -3.314 9794 10224 230628
result: LaBrana1 HungaryGamba_HG Spanish Ust_Ishim -0.0262 -4.069 9201 9696 230134

Chad Rohlfsen said...

Matt,
Wrong link, sorry.
Here you go.

https://docs.google.com/document/d/1kDU5rPpYySUVVIDkdA-UpOKkdmqPehKJg4v5YNIhRrc

rozenfag said...

Hello, I'm not sure whether it's interesting for you, but I made a map with locations of remains analyzed in Haak et al: https://www.google.com/maps/d/viewer?mid=zPTFaw2rnx-E.kfoCf5XA8Lgw

I also included possible results of DNA analyses in the future: https://www.google.com/maps/d/viewer?mid=zPTFaw2rnx-E.kfoCf5XA8Lgw

postneo said...

@davidski

Yamnaya as EHG/Georgian/Kalash

0.490 0.532 -0.023 infeasible

Yamnaya as EHG/Georgian/Pathan

0.491 0.539 -0.030 infeasible


it looks like a pathan like component is amply represented by georgians besides other yamnaya like features not there in pathans. This is expected since kalash and pathans are far more distant populations.

georgia has been iranized , under roman rule and also under mongol influence during its known history.


Davidski said...

posteno,

Which uniparental markers in the Yamnaya and modern Europeans would you correlate with this Pathan-like component?

Nirjhar007 said...

@David
''Very interesting read...''
I think if one day the profs able to yield aDNA from Maykop horizon they will get a more substantial amount of Indian type ancestry with Yhgs like of R1b and probably R1a too but I also think that R1a probably had a more North Eastern Root like the Jarmo one towards Urals starting from 6000 BC and Before, On Kazakhstan aDNA from Chalcolithic if possible it will also have similar out come but with more WHG type ancestry and of course High levels of ANE.
Now on PIE i think within the Zarzian-Zagros horizon this culture of Turkemenisthan had a significant role in IE languages spread -
http://www.britannica.com/EBchecked/topic/302413/Jeitun

Mike Thomas said...

David, Nirj, PN

Has anyone looked closely at modern R1b distribution in South Central asia ?

From what I know , it's only up to 10% and is almost all Z-2103 ?

Nirjhar007 said...

Mike Bud, Not very sure on R1b in the Subcontinent which is a R1a and R2a area and R1b appearing in Pockets rarely but there is as you know an interesting case from Bhutan-http://www.molgen.org/eng/viewtopic.php?t=1857&p=23174

Alberto said...

@Davidski

I don't usually make strong cases for uniparental markers, because especially in ancient times with low population densities they could be subject to strange coincidences or randomness. But let's see if this makes sense:

The theory is that both populations (ANE and EHG) come from the same origin. MA-1 was identified as an ANE, and he was carrying R1. I actually think that he was still neither ANE or EHG, but a population ancestral to both (though probably more in the way of becoming an EHG).

My guess is that the population that stayed in Central Asia (probably including Kazakhstan, as you suggested) were the ones that became ANE some thousands of years after, while the ones who continued further north (Siberia and EE) ended up becoming EHG.

Kazakhstan was still a zone of contact, which might be why EHG retained a large amount of ANE and ANE retained some smaller amount of WHG. In any case, having MA-1 as R1, and by modern distribution, both populations probably shared the R1 Y-haplogroups.

However, the Near Easterners who expanded to the east seemed to be predominantly J2 (Mesopotamia? West Iran?), in contrast with the G2a from the ones that went to Europe (Levant? Anatolia?), bringing this haplogroup to Central Asia, along with other Near Eastern mtDNA haplogroups (H?). Difficult to say which mtDNA haplogroup was native to them, since it's a strange mix these days.

Davidski said...

Alberto,

MA-1 belonged to R*.

Alberto said...

Ah, my bad then. I didn't check and was sure that he was R1 already.

In any case, R1 still seems the best bet for this ANE population. Though with haplogroups I'm always ready to be surprised.

Talking about Macedonians (where I live now), they (and other Balkans populations) have a lot more E1b1b than in Spain, yet they have less (if any) north African admixture. Basques and Catalans have highest R1b, but lowest Steppe admixture (and none were IE speakers when Romans came). Haplogroups can be a bit random, so it's better to rely on aDNA when available.

Davidski said...

One of the best models I can find for Armenians:

Yamnaya 0.110

Stuttgart 0.890

std. errors 0.055, tail prob 0.870589

Davidski said...

Models involving Pamir Tajiks and Pathans + Stuttgart are almost as good as the one with Yamnaya, but not as good.

Alberto said...

Interesting.

And is the reverse true for Georgians? I mean, do they fit better as Tajiks + Stuttgart than Yamnaya + Stuttgart?

That would be a good clue if true.

Davidski said...

Georgians also look better as Yamnaya + Stuttgart than Pathan/Tajik_Pomiri/Sindhi + Stuttgart. This is actually one of the best models for them...

Yamnaya 0.217
Stuttgart 0.783

By the way, the best model I've come across for Pathans to date is...

Yamnaya 0.470
Starcevo_EN 0.432
Dai 0.098

As far as I can see, it's not a bad fit. But I think it's overestimating the Yamnaya-related input due to a fairly poor Neolithic reference.

Shaikorth said...

Can Stuttgart or other EN reference be replaced with Samaritans or BedouinB for Armenians and Georgians? An EEF+Yamnaya fit feels a bit too WHG-like considering their positioning on PCA's even if it's plausible F-stat wise.

Alberto said...

Pity, a different result for the Rb1 and IE speaking Armenians and for Non-IE and not R1a/b Georgians would have been very telling.

But I guess the better fit it's just related to Yamnaya containing the original ancient population from where Georgians and Armenians descend, while Tajiks/Pathans are distant relatives of that original population.

It's pity that the DNA they took from Kazakhstan is only 3000-4000 years old. If they had gone a bit more back in time they could have found a key unadmixed population.

Mike Thomas said...

@ Dave / Alberto

I think our hypotheses aren't exactly too divergent. We're merely debating about the nitty -gritty of the location, directions and degree.

My view is that the Copper Age was actually various different population movements in which the steppe was one part, and the "Yamnaya-like" ancestry seen across wide-spread parts of Eurasia is a still yet to be fully resolved.

@ Alberto

"Macedonians ... and other Balkans populations have a lot more E1b1b than in Spain, yet they have less (if any) north African admixture"

That's true. But its because the E1b Balkan peoples have (specifically E-V13) is an ancient, pan- Mediterranean signature which spread by the Neolithic, and possibly earlier in the Mesolithic. The type predominantly found in modern Iberia is indeed North African, having spread recently by Moors, etc. As you say - a classic case of the same Y sub-haplogroups representing otherwise very different populations.

Re: R1b & Latin peoples: You're right. The Italiana and Iberians have high levels of R1b yet they are not at all a 'northern people', autosomally. They remain clearly west Mediterranean after all these thousands of years. I think different processes occurred in southern and southeastern Europe during the Bronze Age c.f. the North. Today, Balkan Slavs are relatively northern compared to the peoples which would have lived in SEE during the Iron Age and prior.

Davidski said...

Shaikorth,

The models using BedouinB aren't as good, even if I remove the Yoruba from the "right set", which is what I should be doing, because Bedouins have some Sub-Saharan ancestry from a population like the Yoruba.

Stuttgart and Starcevo_EN are clearly better references. I suspect this is because the f4 stats go deep into the phylogeny, so they go beyond the differentiation between similar components like the European WHG and WHG-like from the Near East.

Alberto said...

@Mike

"But its because the E1b Balkan peoples have (specifically E-V13)"

Yes, thanks for the correction, I should pay more attention to subclades. E-M81 seems to be the North West African one that is present in Iberia at higher levels.

By the way, the paper about BMAC was very interesting in how it explains interactions, acculturation and changes in the way of life to adapt to changing environments beyond a simpler model of confrontation/replacement.

Shaikorth said...

If SSA affects the fit, perhaps it's worthwhile to try Lebanese Christians in place of Bedouins?

What Nick Patterson said about qpAdm:

"Users have to supply a list of
"left" and "right" populations, and if there were funky migrations between left and right
after the admixture event of interest it won't give the right answer."

Doesn't this mean just that there shouldn't be recent admixture between the "right" and "left" groups, and not between them and the source populations? So no Chukchis and Ulchis in right and left group respectively, but Yoruba in one group when BedouinB is a source population doesn't matter.

Nirjhar007 said...

@Alberto
The split of R into R1 and R2 most likely happened in SC Asia or very close to it....

Davidski said...

Shaikorth,

I don't have Samaritans or Lebanese Christians in this dataset. I can put them in at some stage, but I have the Iraqi Jews here, who are probably on a par with the Lebanese Christians as Near Eastern references, because they have low ANE and SSA admix, and they don't work as well as Stuttgart and Starcevo.

Mike Thomas said...

@ Alberto

Naturally, understanding what happened in BMAC is required for revealing Indo-Iranian in central -> southern Asia. What Kohl describes (already apparent) is that our current models fail to explain central Asia because there has been no evidence of an invasion from the steppe. Now, genetics might prove it in the future, but that's another story.

But Kohl makes one very important point. The region *east* of the Caspian was largely desert, making contact between the Ural and Volga steppe begin later compared to that on the western end, through the Caucasus, which began early (c. early M 4 BC), and earliest of all, with the Balkans (c. M 5).

Mike Thomas said...

As you know, the desertification of central Asia occurred mid Holocene, so sometime c. 7000 BC, and not reproached until 2300 BC.

Alberto said...

I think that Starcevo_EN is the closest we have to ancient Near Eastern populations. All modern ones are heavily admixed. Sub-Saharan might not even be the biggest problem, but they all have large amounts of West Asian (30-45%), that even if it doesn't translate into high ANE it is an intrusive admixture of some kind (maybe a different kind of Basal Eurasian or whatever).

Alberto said...

@Mike

"As you know, the desertification of central Asia occurred mid Holocene, so sometime c. 7000 BC, and not reproached until 2300 BC."

I'm still wondering about how precise this is. Information about the level of desertification at that time is not very clear (unless you found some good study about it).

If indeed it was very arid since so early, where could a big population be found? We do need a big population somewhere between Iran and Kazakhstan (or probably all of that area together). Small, dispersed populations wouldn't make it possible to have such big impact in already much bigger and populated areas (unless we resort to the legendary warriors killing 1000 men each and having offspring with 1000 women each).

Also, if it was so arid since so early, the population needn't migrate (if they were adapted to such conditions).

Alberto said...

@postneo

"I think its the best bet. It also has to be an area neighboring Yamnaya. We don't have to imagine them as a homogenous population but separate ones from both siberia as well as areas south of turkmenistan that aggregate near Yamnaya."

Ah, I missed you comment till now. Yes, probably not a single population, but ones from different places with a few common traits.

"I have not sees a single map of EHG distribution."

There was a K9 spreadsheet with an EHG cluster. It was high in all of Siberia and decreasing when entering Europe, being at low levels till Ukraine/Poland and then only traces. In Central Asia is was low, and quite related to Turkic admixture, mostly disappearing as you went south.

postneo said...

@davidski
"Which uniparental markers in the Yamnaya and modern Europeans would you correlate with this Pathan-like component?"

In modern georgians the pathan like link seems to be r1a (mostly z93) and r2a and also represented by mtdna u, w

Please note that the georgians are a proxy for "yamnaya like" Not the real population. It could even have gotten more yamnaya like due to more recent migrations from Iran/west asia and europe.

as for markers btw europe and georgia, it would be r1b, G and mtdna like u1, u2, u3, w. Except for u3 the mtdna lineages are very old and were diffusing for longer than than corresponding shared y.

r1b in south asia has not survived except in more mountainous regions.

In fact there is no unbroken trail of y lineages between europe and south asia, rather a chain. the mtdna lineages are similarly not continuos

There was no singular farmer wife event but in general mtdna diffuses more and ties greater geographical regions together than y lineages.

Alberto said...

I went back to that article where Nick Patterson said they took DNA from Maykop. They quoted him saying this about the origin of IE languages:

"Genetic evidence ruled out one likely related group in the region, the Yamnaya, because their DNA showed the group had hunter-gatherer ancestry, which is inconsistent with the fact that two Indo-European groups, Armenians and Indians, don’t share it, Patterson said. That made Patterson look south, to the Maikop civilization, which likely had significant contact with the Yamnaya, as a plausible culture where Indo-European languages originated. Samples have been obtained from Maikop burial sites, but the DNA work to test that proposal is pending, Patterson said."

I doubt that Nick Patterson expressed himself in those exact terms, or if he did it was because the audience (or the journalist) needed a simple explanation.

But what I understand is that after seeing the EHG and Yamnaya samples they realized that it was the "Armenian-like" population that had a genetic profile that could better fit into all IE populations, including Asian ones, while EHG couldn't without many constraints. And being that population already part of Yamnaya it made sense that IE languages might have come from them. So they're now looking for that "Armenian-like" population. First in Maykop. And then beyond (weren't they going to Iran and India?).

The paper is more cautious and presents both hypotheses (Steppe and Armenian plateau) as gaining plausibility against the Anatolian and Balkan ones. But it seems that they are really looking into the Armenian one as their best option.

Nirjhar007 said...

@Alberto
''Genetic evidence ruled out one likely related group in the region, the Yamnaya, because their DNA showed the group had hunter-gatherer ancestry''
Really? Nick really suggested that? or is it a lie?

Alberto said...

I think that the article was poorly written and it's an oversimplification of what he said. But here it is:

http://news.harvard.edu/gazette/story/2014/12/the-surprising-origins-of-europeans/

Nirjhar007 said...

@Alberto
Thx. Anyway i think Nick should clarify to us.

Davidski said...

Nirjhar,

He already has explained it.

And the latest on the issue is in Haak et al. which you've read.

postneo,

Surely you must realize by now that R1a is a poor candidate for such a marker, and so is its sibling R1b.

postneo said...

@davidski

why is it a poor marker? What is a good candidate according to you. What exactly are you looking for?

As for other ones theres j2b as well. This one correlates somewhat with r1b in the Indian subcontinent but has better survival. There very little g in India.

postneo said...

@davidski

so in general modern georgians have modern south asian like lineages

J2, L, R1a(z93), R2a on the y side U, W mtdna which makes them adequate in representing a south asian component.

Davidski said...

posteno,

Why do you keep mentioning R1a-Z93 in this context? Do you know something that rest of us don't, or are you just going by modern frequencies?


Nirjhar,

Here's a more recent quote on the topic from another university gazette.

"Particularly if we want to nail this hypothesis and put a geographical homeland somewhere in the steppes in Ukraine or Southern Russia, then we would assume that whatever was brought by these people would also be found in other populations that today speak an Indo-European language," Dr Haak said.

"That is equally likely for people further in the East, if you go to Iran or India. Currently we've only focused on Europe, but that equally applies to those regions as well. Now we have to look at both ancient and modern day Indian populations."

http://www.theleadsouthaustralia.com.au/industries/research-development/ancient-skeletons-hold-the-key-to-origins-of-the-spread-of-indoeuropean-language/

postneo said...

ok g is found in south asia. among brahui, baloch, less in pathans, Its been found in sri lanka strangely. otherwise rare. This needs to be studied more I think.

spagetiMeatball said...

Where are they going to get samples in south asia? Is there anybody well preserved there? Maybe from the cemetery H culture.

Krefter said...

@postneo,

"As for other ones theres j2b as well. This one correlates somewhat with r1b in the Indian subcontinent but has better survival. There very little g in India."

I'd wait till you have a huge and very well organized data set of Indian Y DNA to take any position. To me haplogroup frequencies aren't very significant, I think we need to look deeper.

Krefter said...

@Davidski,

Do you think there's significant Steppe ancestry in south-central Asia? Your recent tests suggest this, but how does "South Asian"(ANE rich?)-specific ancestry affect this since it isn't put in the equation? IS South Asian ancestry combined with ENF being confused with Steppe?

If there is something like 30-40% Steppe ancestry in central-south Asia, we should expect to see Yamna-like mtDNA not just Y DNA there.

postneo said...

@david

Why do you keep mentioning R1a-Z93 in this context? Do you know something that rest of us don't, or are you just going by modern frequencies?

Because the Georgian samples are modern as well. So you should compare apples to apples.

Are you telling me that the georgian data was screened for z93 somehow? If that was the case then you would find yourself bumping up the Kalash/Pathan component (also modern by the way)

Not just z93 but some of the others I mentioned INHERIT and carry ANE and ASI which we are trying to explain.

Grey said...

@Alberto

"where could a big population be found? We do need a big population somewhere between Iran and Kazakhstan"

Why big?

If the Central Asian connection is early foot herders expanding over HG populations into the near east they only need the leading edge of the expansion to have a larger density than the HGs.

Or are you talking about an alternative to a copper age steppe expansion? In which case the same argument applies as applies to a steppe expansion before cavalry - mounted raiding is effectively guerrilla warfare so over time would (imo) lead to the raided region depopulating allowing the raiders to simply move into the no man's land they created.

Grey said...

"Georgians also look better as Yamnaya + Stuttgart than Pathan/Tajik_Pomiri/Sindhi + Stuttgart. This is actually one of the best models for them...

Yamnaya 0.217
Stuttgart 0.783

By the way, the best model I've come across for Pathans to date is...

Yamnaya 0.470
Starcevo_EN 0.432
Dai 0.098"

So making up a model for fun...

if a foot herder population expanded out of Apple Valley in Central Asia into India, Iran, Near East and SE Europe and later a mounted herder population expanded out of the steppe then the model combined with the above would be...

Starcevo as the CA foot herders
Yamnaya as Yamnaya
and
Stuttgart as Starcevo + some WHG

Alberto said...

@Krefter

"but how does "South Asian"(ANE rich?)-specific ancestry affect this since it isn't put in the equation? IS South Asian ancestry combined with ENF being confused with Steppe?"

Probably yes. It could be tested dividing Yamanaya into EHG + Georgian. For example:

Pathans:

Yamnaya 0.470
Starcevo_EN 0.432
Dai 0.098

Would modelling them as EHG + Georgian + Starcevo_EN + Dai give something like:

EHG 0.24
Georgian 0.23
Starcevo_EN 0.43
Dai 0.1

Probably not. Georgian might go up and EHG down, not maintaining the same Yamnaya proportions. Or maybe yes, who knows.

postneo said...

@krefter

I did not quite understand what you mean by south asian samples need to be more organized.

Perhaps you are saying that the statistics are poor since the samples are not representative given large population.

Or are you saying the act of modern south asian sampling or somehow the dna itself is inherently more disorganized as compared to that in modern Georgians?


@grey
What is meant by foot herder. All pastorialists in the old world herded on foot. There were no cowboys and gauchos in the old world. mounted cavalry is from the late bronze age and were not used for herding. Besides horses all domestic ungulates are slow animals.

the steppes acquired early pastorialism from Iran and caucasus. Why because goat and sheep genetics points to domestication there. turkmenistan is not a suitable place for wild goats. kyrgyztan and tajikistan are OK places for it.

Cattle domestication occurred in the anatolia and south asia not the steppes.

The Steppe people ate horseflesh and herded/hunted horses. Perhaps they started riding to capture more horses bit otherwise not useful for herding.

Grey said...

@postneo

"What is meant by foot herder"

It's supposed to mean herders who didn't have horses yet.

.

"kyrgyztan and tajikistan are OK places for it"

Yes.

.

"The Steppe people ate horseflesh and herded/hunted horses. Perhaps they started riding to capture more horses bit otherwise not useful for herding."

Yes, mounted hunters.

.

"the steppes acquired early pastorialism from..."

Yes, mounted hunters + foot herders
->
foot herders with mounted elite

(imo)


"Cattle domestication occurred..."

Yes, cattle later.

Mike Thomas said...

@ Alberto

Sirianidi argues that there was indeed very dry conditions in CA in M9 -8 . Scattered early farming communities existed in west central Asia by M6, with increasing population during the next 2 thousand years, with evidence of wide-spread contacts necessitated by a resource-poor ecology.

But the fact remains, large parts of Kazakhstan were desert. Whatever contacts were elaborating and dispersing from central Europe, to northern India, must have occurred via somewhere else prior to late M3. This only leaves the Caucasus and eastern Balkans. I have my hypotheses, and they don;t include a simple scenario of arrows spreading ex-Yamnaya. Im sure aDNA will prove me right.

@ Post-Neo

"there were no cowboys and gauchos in the old world. mounted cavalry is from the late bronze age and were not used for herding"

Grey seems unable to digest simple facts, in this matter.


"the steppes acquired early pastorialism from Iran and caucasus. Why because goat and sheep genetics points to domestication there. turkmenistan is not a suitable place for wild goats. kyrgyztan and tajikistan "


Partly true - for the eastern steppes, via Tien- Shan region. The central steppe was more or less an indigineous development based largely on horse hunting to gradual horse domestication.

On the western steppe, cattle and pig dominated, from a clearly SEE origin.

Mike Thomas said...

Im sure people have come across this book

http://unesdoc.unesco.org/images/0009/000944/094466e.pdf

Nirjhar007 said...

@David
Hi!
''Here's a more recent quote on the topic from another university gazette.''
I know about that article but it is just that Nicks remarks were pretty strong and i would have liked his personal opinion here if possible,
Anyway the actual thing is that since Southern Russia is the ''popular'' ''candidate'' the onus of course was to study there first and then to make interpretations on ''assuming'' it as the ''possible source'' of PIE but obviously the model is not much of a success at all Outside Europe and even within some important IE Populations of Europe.
We have to get aDNA from various geographical Zones of Eurasia and then have to compare which aDNA pattern works ''comparatively best'' like from Central Asia,Balkans,Anatolia,India, North Iran-Armenia then we may reach a satisfactory outcome....

Mike Thomas said...

Nirj
I think his comments in the article were pretty clear, actually.

Davidski said...

I'd say Haak's comments in the article I linked to were pretty clear too; they're going to try and get ancient DNA from India to see if they can, and I quote, "nail" Ukraine/southern Russia as the PIE homeland.

Nirjhar007 said...

David,
Yes it appears he favors that.

Mike Thomas said...

That's great news

Chad Rohlfsen said...

So far, best fit for Motala is
82.5% Loschbour
17.5% Karelia

Std .135 p-value about 1.75. It may not get better than this. I've got a few for Loschbour and I'm also working on another big project. I'll post my findings after conferring with Nick.

Nirjhar007 said...

@Chad
If i'm not mistaken u r going to that Aegean aDNA conference, so if allowed and possible will u be able to do a video recording for us??

Mike Thomas said...

Thanks Chad
So it looks like SHG is essentially WHG with a touch of EHG ?

Davidski said...

Nirjhar,

I hope you're not accusing Haak of being biased. He's simply testing the most popular hypothesis in regards to the PIE homeland.

I'm pretty sure nailing it wouldn't bring him any more joy than disproving it. But I'd say the general feeling is that it probably will be nailed sooner or later with the help of aDNA.

Nirjhar007 said...

@David
''I hope you're not accusing Haak of being biased''
No of course not.
''I'm pretty sure nailing it wouldn't bring him any more joy than disproving it.''
of course.
'' But I'd say the general feeling is that it probably will be nailed sooner or later with the help of aDNA.''
That's a little ''overconfident'' statement in ''reality'' we have still a long way to go and have to face good amount of outcomes and variabilities....

Chad Rohlfsen said...

Nirjhar,
I'm pretty sure they won't allow video, but I will be posting everything here.

Nirjhar007 said...

@Chad
Of Course! but do keep that option alive unless u r 100% sure:).

Alberto said...

Did we ever get to know reliably which Hinxton genomes were Iron Age and which ones from the Anglo-Saxon invasion time?

Might be interesting to see if there's any difference in Yamnaya admixture. Probably Hinxton1 (Anglo-Saxon?) vs. Hinxton4 (Celt?) as:

Germany_MN
Yamnaya
Loschbour

Alberto said...

@Mike

Did you by any chance get to some concept of PIE "network" (not sure if that's the right word) as opposed to "homeland"?

Something that around 4000 BCE might go from Tien-Shan to the Eastern Balkans through the south coasts of the black and Caspian seas?

Or something totally different?

Grey said...

A different take on my pet obsession with the "giants".

I think there's some archaic aspect to ANE (mainly a gut feeling I admit) and I was thinking multiple surviving populations and multiple introgressions but actually a much simpler explanation would be the same neanderthal / denisova introgression already generally accepted but variable survival rates of the archaic genes among different populations.

That is if the initial mix must have been 50/50 and the N/D genes were adapted for a cold, boreal environment then the mixed human population might have lost the N/D genes at different rates depending on their environment.

So by the time people in the middle east were at say 4%, maybe people in Scandinavia, Tien Shan, Karakorum etc were still 20%.

Srkz said...

All difference maps: https://www.dropbox.com/s/5daq1sze9cylalm/IBDmaps.zip?dl=0

Srkz said...

PS Warning - file size is over 65 Mb

Mike Thomas said...

@ Alberto

Did you by any chance get to some concept of PIE ...."

Yes Im working on it Alberto. I have a pretty solid idea, I think. Will keep you informed. :)

Krefter said...

Davidski, can you run West German, South Dutch, and your Swiss sample through Yamna K6?

Variation in France seems to be mostly Yamna vs pre-Yamna, and I'm wondering if south-west German speakers follow the same pattern.

Nirjhar007 said...

@Mike
''Yes Im working on it Alberto. I have a pretty solid idea, I think. Will keep you informed. :)''
I suspected this and let me tell i can hardly wait!:)

Chad Rohlfsen said...

British origins paper.

http://dienekes.blogspot.com/2015/03/british-origins-leslie-et-al-2015.html?m=1

Helgenes50 said...

@ Krefter

Variation in France seems to be mostly Yamna vs pre-Yamna

Where did you see these results ?

Alberto said...

@Mike

"Yes I'm working on it..."

Looking forward to it too :)

Davidski said...

Comparing Indo-European and Semitic neighbors Armenians and Assyrians, respectively.

Armenian
Yamnaya 0.110
Stuttgart 0.890

Assyrian
Yamnaya 0.079
Stuttgart 0.921

Both are good models, but the Assyrians also work well as just ~2% Yamnaya.

And Pathans as a four-way mix of EHG, Georgian, Starcevo_EN and Dai is a failure, unlike the three-way that worked really well (Yamnaya, Starcevo_EN, Dai).

Alberto said...

@David

"And Pathans as a four-way mix of EHG, Georgian, Starcevo_EN and Dai is a failure, unlike the three-way that worked really well (Yamnaya, Starcevo_EN, Dai)."

Strange that substituting Yamnaya for EHG+Georgians turns a good match into a failure. I guess that it proves how much better ancient samples are compared to using modern pops to substitute them.

Somehow related to this: did you try to model Yemenite_Jew or BedouinB as something like:

Starcevo_EN
Maasai
Pathan

To have an idea about their level of admixture?

Davidski said...

Yeah, these seem to work. But of course both the Masai and Pathans have a lot of Near Eastern ancestry.

Yemenite_Jew
Starcevo_EN 0.396
Masai 0.137
Pathan 0.467

BedouinB
Starcevo_EN 0.335
Masai 0.150
Pathan 0.516

BedouinA
Starcevo_EN 0.239
Masai 0.201
Pathan 0.559

Davidski said...

Here's another decent fit for Pathans.

MA1 0.250
Starcevo_EN 0.643
Dai 0.107

This is worse, but the MA1 figure matches the ANE estimate for Pathans in my K8.

MA-1 0.353
BedouinB 0.501
Ami 0.146

Nirjhar007 said...

David,
We of course don't know very much of what kind of Study has been made but what are your expectations from the Aegean aDNA in Autosomal and hg's point of view?

Davidski said...

I think that one of the things they'll say is that the mtDNA structure in the Balkans changed from typically Neolithic to basically what we have there today during the Bronze Age, and that this happened due to a migration, or a series of migrations. If so, then I guess they might point to a possible source of this migration using the full ancient mito genomes they've collected.

I don't know what else they tested, so I can't add much more. But I'm sure Chad won't miss a single detail in his report.

Mike Thomas said...

David
* so are your results suggesting that Georgians are simply a two wave mix of a EEF type, Stutgart-like group and a Yamnaya group (which itself is half EHG; half Georgian like) ?

Alberto said...

Thanks David.

Yes, Pathans especially have a lot of Basal Eurasian. But as you speculated it seems to differ in some way from the one in EEF.

Pity we don't have any ancient DNA from the NE, nor a precise idea of where EEFs came from. Maybe the Near East was not so homogeneous. Let's hope the attempt of getting Sumerian DNA is successful.

Nirjhar007 said...

@Kristiina, Jaska
If you guys are reading my suggestion is that Uralic people colonized lands inhabited
by Aryans (as happened in Hungary in the Middle Ages), that's why they called slaves 'oryo'.
It would be a reversal of the common view of imperialistic Aryans! :)
What you think?

Nirjhar007 said...

@David
Sounds Great.

Nirjhar007 said...

Alberto,
''Let's hope the attempt of getting Sumerian DNA is successful.''
Well isn't the sample count is 1 or is it 2? I don't think its going to be enough, what if they were merchants/Travellers from somewhere else??:)

Mike Thomas said...

@ David , Nirjahar

Yes that talk on Greece will be great. I'm sure Chad is looking forward to it.
I wish they also got autosomal and Y data. But I know it's very difficult.

Nirjhar007 said...

Thank you Mike for adding another dimension to my name!:D

Gökhan said...

A simple question, If so called ANE which is carried by Georgians and Lazs came through South Caucasia from Yamna why do Georgians lack of WHG? If i am wrong correct me please. Isnt WHG in Yamna is quite higher then Georgians and Lazs?

In my opinion ANE should be separeted into two piece, Gedrosa and Ancestral Altaic. ANE in georgians is Gedrosa companent, ANE in yamna mostly realted with Amerindian + Gedrosa combination.

Thus in my opinion the "ANE" in southern caucasia" is not the "ANE" Yamna have. Caucasia mountains was a great barrier for horses.

Gill said...

"Genetic evidence ruled out one likely related group in the region, the Yamnaya, because their DNA showed the group had hunter-gatherer ancestry, which is inconsistent with the fact that two Indo-European groups, Armenians and Indians, don’t share it, Patterson said. That made Patterson look south, to the Maikop civilization, which likely had significant contact with the Yamnaya, as a plausible culture where Indo-European languages originated. Samples have been obtained from Maikop burial sites, but the DNA work to test that proposal is pending, Patterson said."

Later WHG-less migrations of ANE/ENF-rich West Asian populations could explain the turnover, but they retained the older Indo-European language/culture. Especially since there's a scattered pattern of remnant WHG throughout Eurasia and p-possible evidence of multiple Steppe/Central Asian populations moving around.

For instance, the extra Caucasus admixture we see in areas east of Iran (especially Afghanistan) could be from an Indo-European population that had low WHG, but the relatively higher traces of WHG in proportion to ENF in some groups (Tajiks, Haryana India) could be explained by a more WHG-rich population. Which could be evidence of multiple "cousin" Indo-European population migrations. The reason for a small WHG hotspot in Afghanistan in spite of that could be that the source was very recent (as per local tradition as well). Meanwhile the source for North India could be really ancient (quite likely) and possibly had more WHG to begin with.

Digging up lots of ancient aDNA from the various IE cultures in South/Central Asia (not just one) would be key. Otherwise they're all obviously going to be related to one another to some substantial but vague degree.

Mateus Smith said...

Something caught my attention while reading about the new study on British genetics:

"The migrations revealed in that way match the known historical record but also point to events that have not been recorded, such as a major migration from northern France that accounts for about one-third of the ancestry of the average person in Britain."

Source: "Study Reveals Genetic Path of Modern Britons."

http://www.nytimes.com/2015/03/19/science/study-reveals-genetic-path-of-modern-britons.html?partner=rss&emc=rss&_r=1

Would this explain why modern British people are more southern compared to the Hinxton genomes?

rozenfag said...

@ Mateus Smith
I looked up quickly this paper and it seems they didn't compared modern genomes with the ancient ones. So I am not sure how reliable are their conclusions about migrations.

Grey said...

@Mateus Smith

"a major migration from northern France"

If they're comparing the genes with modern northern France then those genes could be from ancient western Germany.

or

if it was older that that then maybe Belgae?

Hopefully someone will be able to add some time stamps to at least some of the components which might help to figure out a sequence.

rozenfag said...

By the way, i found this news: http://www.newscientist.com/article/mg22530134.200-red-lady-cave-burial-reveals-stone-age-secrets.html?full=true

19 000 years old remains of a woman from northern Spain will be analysed by Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig.

Apparently it will be very interesting!

Krefter said...

Thanks a lot for the article rozanfag!! I wish they choose a man to sample so we can get a Y DNA result from Upper Palaeolithic west Europe(without a doubt would be hg I).

If the "Red Lady" doesn't come out U5b and pure-WHG autosomally we'll all be very surprised.

There's two mtDNA samples listed on Jean's site from Spain that are around the same age as the "Red Lady".

http://www.ancestraljourneys.org/palaeolithicdna.shtml

One is an unknown R with two mutations passed rCRS, and the other is U5 with two extra mutations: 16311Y(why Y instead of C?) and 16270C!(I don't know if that marker was tested or not). It lacks 16256 so we can confidently say it isn't U5a.

The study is from 2005, that makes it more likely the results aren't legit though.

U5b2a1 is the only U5 clade with 16270C!, but this sample lacks 16189C! which is needed to be U5b2a. 16189C! mutates often and thid sample lacking it doesn't take away the possibility of it having U5b2a1. pre-U5b2a1a1 is defined by 16189T!! and 16311C!, so this sample could also be apart of that lineage.

Mike Thomas said...

Krefter
"without a doubt would be hg I"

I bet it'll be Y Hg C

Krefter said...

Mike,

La Brana-1 and the few Neolithic Hungarians are the only examples of C(V20) we have from Stone age Europe. Counting Neolithic hg I, there's something like x6 more I.

Mike Thomas said...

I agree
But Kostenki was C and I think C came first .
Then I swarmed in from SEE either after or just before LGM

Alberto said...

I came across this paper about Lactase Persistence in the Neolithic Basque Country. It seems that from 19 samples from a 5000 ybp site there were 31% with Lactance Persistence (and a total of 27% including samples from another site from 4500 ybp). Quite in contrast with the paper from the other day were they say the first sample in Europe with LCT was a Bell Beaker from Germany from 4300 ybp.

http://www.nature.com/ejhg/journal/v20/n7/abs/ejhg2011254a.html

Krefter said...

@Mike,

I'm not an expert on Y DNA I, but experts say it's probably been in Europe for around 30,000 years. U5 is shared by EHG and WHG, and an over 25,000YBP Czech. Saying WHG-related(also existed in EHG) ancestry was already in Europe 19,000YBP is reasonable.

capra internetensis said...

@Mike

Many people associate the expansion of hg I with the Gravettian (right time and right place), but what post-LGM expansion did you have in mind?

Mike Thomas said...

@ Capra & @ Krefter

"most people associate expansion of Hg I with Gravettian" and is "30 000 years old"

Yes, most people do. But not on any definitive evidence. Whilst certainly possible, the issue is complex. Indeed, the only yet sequenced UP specimen from Europe - Kostenki - associated with Gravettian material moreover- was Hg C. That WHG -related groups were present in Europe 19kya doesn't mean that Haplogroup I clades have been. And, remember that Haaks study showed that Kostenki was more WHG than EHG - related.


In fact, the issue is even more complex. Given the absence of actual hominid remains with the large majority of Gravettian assemblages, and the otherwise complex stratigraphy in sites eg Vindaja Cave, Croatia, not everyone is happy to automatically assume Gravettian automatically = AMH 'suddenly and 'rapidly' fanning across Europe.

Now, Im sure that Hg I is indeed 30kya, but where it was exactly 20 kya is a different story. Ie- was it yet in central -western Europe ?

Anything is possible. So a few samples of UP remains is yet another thing on the wish list.

Karl_K said...

"I wish they choose a man to sample so we can get a Y DNA result from Upper Palaeolithic west Europe(without a doubt would be hg I)."

I don't think they really have much of a choice. However, just because they call her the red lady doesn't mean she is female. In the paper describing the bones, they say she is "probably female".

capra internetensis said...

@Mike

The Kostenki region is well known for its Eastern Gravettian remains, but Kostenki-14 himself is 36-39 thousand years old, well before the Gravettian proper. Some people do think this period at the site represents some kind of proto-Gravettian, others consider it Aurignacian, or neither. Either way, K-14 is a good deal earlier than the estimated expansion time of Y hg I, and really any Gravettian identification is debatable.

And yeah, more UP aDNA would really help.

Mike Thomas said...

Capra
You're correct. I didn't recall the specifics of K14 quite accurately .
Nevertheless, my main point is that C is likely to be earlier than I in Europe , and perhaps sill the dominant lineage until the LGM

Kristiina said...

Nirjhar, I just had a discussion about the new haplotrees in the new paper ”Bottleneck in human Y-chromosomes in the last 10,000 years” (http://genome.cshlp.org/content/suppl/2015/02/18/gr.186684.114.DC1/Supplemental_Figures.pdf)

On the basis of the haplotrees and age estimates, the centre of expansion of N1c and N1b looks quite western (west of Urals) and, even more so now that we know that N1c was in Smolensk 2500 BC. Jaska is adamant that N1c men in Smolensk did not speak a Uralic language. I am not so rigid. I think that he may very well have spoken a kind of Uraloid language. However, it is possible that when N1c L550 or whole VL29 arrived in Finland, these men had changed their language or their language had evolved into a Corded Ware type of language. Yet, it is equally possible that VL39 spoke another Uraloid language in direct line from the language spoken by the Smolensk man.

By contrast, N1c Z1936, including the Karelian-Eastern Finnish line, Ugric and Nenets lines, may have been a vector of a ”classical” Uralic language and its expansion could be related to metallurgy. It is very well possible that there was a kind of a Uralic hotspot in Volga Oka area where N1b, N1c-B211 and a slightly later evolved N1c-Z1936 may have thrived after mixing with original inhabitants. I think that Jaska will agree with me if I say that it is in this area that various Uralic branches, including Ugric and Samoyedic branches, started their expansion to the east and possibly also to Finland in the form of N1c-Z1927.

The Uralic part of N ends here. There are very old lines that are typical of Turkic groups (Shors, Yakuts). Moreover, N1b seems to have spread from Volga to Mongolia, Tuva and Sakha. One quite old N1c branch is typical of Mongols and has probably been detected in Xiognu. This branch spread quite late also to Koryaks and Chukchis.

You proposed that Uralic speakers colonized the areas of IE speakers. I think that IE languages may have been spoken in the Baltic area, and there, IE and Uraloid languages may have interacted to a great extent. Perhaps they were both new arrivals: one from the south and the other from the east. I do not think that IE languages were spoken in Volga Oka and even less around Kama. I am quite confident that those areas were previously inhabited by microblading groups and their languages had Arctic affinities. I would think that similarities between Uralic and IE languages are due to their geographical closeness to each other before their respective expansions. They may even go back to a similar language or at least share a language among their ancestor languages.

Balaji said...

The Haak paper talks about how “Corded_Ware_LN has ancestry from a component that is basal to both European farmers (...) and European hunter-gatherers”. (pdf page 148 of the document). Ryukendo Kendow has interpreted this to mean that the Near-Eastern ancestors of the Yamanya were pure ENF. Davidski has similarly interpreted it to mean a “a higher ratio of the so called Basal Eurasian component and a lower ratio of WHG-related admixture”.

I read it somewhat differently. Corded_Ware_LN has a BEA component that is different from and “more basal” than the BEA component in LBK_EN and other European early and middle neolithic people. Haak have explicitly talked about a different kind of BEA for Kostenki14 on pdf page 113. I believe they have a similar model in mind for the Yamnaya and Corded_Ware_LN.

That the BEA in Yamnaya and and the European neolithic people are different kinds of BEA can be seen in the PCA of Figure 2 (page 22). With respect to EHG the Yamnaya are shifted to the right due to their BEA. Similarly with respect to WHG, the MN and EN are shifted to the right. The percentage of BEA in the Yamnaya is at least as high as in the MN, yet the shift to the right is visibly less for the Yamnaya than for the MN.

The ADMIXTURE plot in Figure 2 (page 22) also shows that BEA in Yamnaya is a different kind from the BEA in EN and MN. The BEA in Yamnaya for K=16 is in the dark green component. For EN and MN, the BEA is part of the orange component.

European neolithic people originated in Anatolia. Armenia, Georgia and the Caucasus are too close to the Levant to originally have had a different kind of BEA. My suggestion is that the more basal BEA found in the Yamnaya ultimately came from South Asia. In support of this, I have a statement by Davidski from a few months ago.

“Yes, for some reason MA-1 flushes out an African-like signal for most South Asians in their lowest f3-stats. That has to be something basal, but maybe it's even more basal than the Basal Eurasian, and linked to ASI?”

http://eurogenes.blogspot.com/2014/07/f3-stats-100-present-day-populations.html

The four populations with the most negative f3 statistics with Yorubans and Mbuti are as follows.

Gujarati1;MA-1,Yoruban -0.00472043 0.000848891 -5.5607
Gujarati1;MA-1,Mbuti_Pygmy -0.00331065 0.000876543 -3.77694

Brahmin_UP;MA-1,Yoruban -0.00467572 0.000866041 -5.39896
Brahmin_UP;MA-1,Mbuti_Pygmy -0.0033646 0.000897416 -3.74921

Pathan;MA-1,Yoruban -0.00462641 0.00082202 -5.6281
Pathan;MA-1,Mbuti_Pygmy -0.00322952 0.00086212 -3.74602

Tadjik;MA-1,Yoruban -0.00459413 0.000864685 -5.31307
Tadjik;MA-1,Mbuti_Pygmy -0.00318023 0.000899337 -3.53619

Krefter said...

Kristiina, when do you think the most popular N1c branches expanded in east Europe? Do think they spread with Uralic languages? Also, do you think proto-Uralics had Siberian-ancestry but the language itself may have not originated in Siberia?

Uralics from around Finland and the Baltic being largely CWC-related admixed makes sense. This is because Uralics in Russia are very similar to people who lived in that area 5,000 years ago(Samara Yamna), while Uralics further west have a lot of Neolithic central-west European ancestry. The overall makeup of Finns and Estonians is little differnt from Balts.

Balaji said...

Davidski,

Could you run the following f3 stats when you get the time? I believe they are in the format that will work for you.

Basque Papuan Greek
Basque Papuan Sicilian
Basque Papuan Tuscan
Basque Papuan Bulgarian
Basque Papuan Croatian
Basque Papuan GujaratiA
Basque Papuan Pathan
Basque Papuan Yamnaya

Sardinian Papuan Ashkenazi_Jew
Sardinian Papuan Armenian
Sardinian Papuan Cypriot
Sardinian Papuan Druze
Sardinian Papuan Tunisian_Jew

Germany_MN Papuan Greek
Germany_MN Papuan Sicilian
Germany_MN Papuan Tuscan
Germany_MN Papuan Bulgarian
Germany_MN Papuan Croatian
Germany_MN Papuan GujaratiA
Germany_MN Papuan Pathan
Germany_MN Papuan Motala_HG
Germany_MN Papuan Basque
Germany_MN Papuan Yamnaya
Germany_MN Papuan Norwegian

Kristiina said...

”Kristiina, when do you think the most popular N1c branches expanded in east Europe?”
Not sure what you mean, but it looks like N1c has mostly expanded in Russians and other similar groups, such as Chuvashes, Bashkirs and Tatars, and in Scandinavia.

"Do think they spread with Uralic languages?"
Many Russians around Moscow and north of Moscow probably spoke Uralic languages. Prussian N1c is probably not Uralic-related but connected to Lithuanian or its Baltic predecessor. Scandinavian N1c could be related to the Finnish coast whatever language they spoke. Chuvashes may be turkified Volga Uralics. Bashkirs and Tatars are Turkic speakers and their ancestors were really multiethnic.

"Also, do you think proto-Uralics had Siberian-ancestry but the language itself may have not originated in Siberia?"
Perhaps they had a portion of Siberian ancestry, but my idea is that a big part of Siberian ancestry comes from the microblading groups. Jaska may be right when he insists that the Uralic protolanguage originated in Volga Oka. I would not say that Volga Oka is Siberia. However, IMO, many Uralic languages have strong Siberian microblading substrates.

”The overall makeup of Finns and Estonians is little different from Balts.”
Yes, and now we have been shown that both R1a and N1c were in the area with a lot of mtDNA H.

Kristiina said...

I did not read correctly your question, but the answer to your question should be found in the age estimates of this recent paper.
The age of N3a3 (VL29+F4134), a clearly western branch (west of Moscow), is 3470-6322 years. The age of the branching of two exclusively Saami lineages is 638-2374 years. The split between the Udmurt and Mari N1c lineages is dated between 2940-6395 years.

Davidski said...

Balaji,

https://docs.google.com/spreadsheets/d/1Kvlw9H8X1stxALkXrBN-gl0DZgaciFjkGdtGJRJvqEE/edit?usp=sharing

Mike Thomas said...

@ Davidski

If I may ask again :

Do your results suggest that Georgians and/ or Armenians are a straight two -way mix of a EEF-type and a Yamnaya group (which itself is half EHG; half Georgian like) ?

(as opposed to more complex 3 way mixtures, etc. )

Davidski said...

Yes, Armenians and Georgians can be successfully modeled as mostly EEF with significant Yamnaya ancestry.

This is very interesting, because I didn't expect Stuttgart, or even the older Starcevo_EN, to be such excellent proxies for ancient Near Eastern ancestry, mainly because of their likely indigenous European admixture.

In fact, Starcevo_EN, which belongs to Y-HG H, also seems like a decent proxy for the Near Eastern admixture in South Asians, where Y-HG H reaches very high frequencies, especially among Dravidian groups.

But things are surely more complex than that, with migrations and back migrations from a wide variety of areas producing the modern Near Eastern gene pool since the Neolithic.

Mike Thomas said...

That is interesting indeed; that Early Neolithic groups should be so homogeneous and dispersed so widely, esp given that some should have come from the Levant, others Anatolia, some took land routes, others maritime...

What do you think of Balaji's idea of south Asian admixture in Yamnaya. Nothing new , as apparent from the admixture plots we've seen, but how would we interpret it ?

Nirjhar007 said...

Kristiina,
Thank You so much for your observations i consider them significant! about your suggestion which is quite popular indeed that'' similarities between Uralic and IE languages are due to their geographical closeness to each other before their respective expansions. They may even go back to a similar language or at least share a language among their ancestor languages.''
I wouldn't say totally wrong but i think its a bit hyped!:) I 'm currently working on PIE and its ''closest'' linguistic relative(s) and after finishing the job i at once will like to have a good discussion with you! so stay prepared;).
And Yes About the Aryan Uralic Words Relations here a nice lecture by Talageri-
https://www.youtube.com/watch?v=WGXSKOXuDoU
I don't support his OIT model BTW but that Lecture is practical....
And from the Lecture I have to verify some Words like Sishu and Kota do they exist in Uralic and what they exactly mean?
Cheers...

Grey said...

http://www.freeworldmaps.net/asia/asia.jpg

if the HG zones were

D zone: East Asia
E zone: African Border Zone i.e. Levant, Arabia, North Africa, large chunks of coastal Europe
CF zone: everywhere else - stretching out of India to the NW
Hyperborea zone: northern interior bordering northern edge of the Carpathians, Caucasus, Tien Shan, Mongolia etc into the Americas.

A sub group in the East Asia zone who developed farming might spread round the East Asia zone.

A sub group in the African border zone who developed farming might spread round the African border zone - maybe mostly by sea.

A sub group who developed farming / herding anywhere in the CF zone might spread rapidly all over the CF zone.

Hyperborea probably wouldn't be suitable for farming initially.

Davidski said...

Mike,

I'm not seeing any unambiguous signals of South Asian ancestry in the Yamnaya.

Rather, I'd say, the Yamnaya had Central Asian or Siberian ancestry which either contributed in a major way to modern South Asian genetic structure, or came from South Asia a long time ago, probably even before MA-1 existed.

To me, it looks like MA-1 has this influence, and so do the Samara and Karelian foragers, especially the one from the Samara.

Mike Thomas said...

Blogger Mike Thomas said...
Dave

You might be right. It might all relate to deep ancestry, which relates to the fact that R1 populations ultimately branched off K/ P/ R groups who must have dwelt in south-central Asia. Question is exactlt when ? and how many times ? (esp if MA-1 was an evolutionary dead end). I cant imagine anything more recent than LGM.

On the other hand, I see evidence for movements from central Asia to south Asia (I.E. BMAC peoples moving to Indus). But to me at least, the origins of BMAC are more or less 'native' (from south / southeast Caspian region), and not in north Kazakhstan, the Black Sea or the Ural chains.

Mike Thomas said...

Davidski

Do we/ you have access to the genome library created by these scholars (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3824117/pdf/main.pdf) who hav 4 samples (2 each from Bronze Age and Iron Age Bulgaria)

If so would certainly be to model them on the basis of Haak's recent paper.

Nirjhar007 said...

@Mike
'' I see evidence for movements from central Asia to south Asia (I.E. BMAC peoples moving to Indus).''
On The Basis of What?

Krefter said...

As there been serious archaeology work done on Central-South Asia from the Neolithic age and before that? I hope there are some bones they can get DNA from because they'll help us learn about the early history of ANE and the strange uniqueness of south Asians.

Davidski said...

Mike,

Yes, those samples are available online, but they don't offer enough markers to be useful.

I know that the same authors have since sequenced genomes from Bronze and/or Iron Age Bulgaria at much higher coverage, but they're yet to be published.

On a PCA of West Eurasia they basically cluster in no man's land just west of present-day Tuscans, suggesting that they carry less ANE than modern mainland Italians, but clearly more than the HGDP Sardinians and Neolithic farmers.

Mike Thomas said...

Nirjhar
I meant on a relative basis
Wasn't the end of Harappan civ associated with shift of settlement to Gangetic plain?. On the other hand, we see BMAC related material appearing in Afghanistan and Indus region ...

postneo said...

In fact, Starcevo_EN, which belongs to Y-HG H, also seems like a decent proxy for the Near Eastern admixture in South Asians, where Y-HG H reaches very high frequencies, especially among Dravidian groups.


H is not near eastern. Its mostly south asian or in some cases west european. H1 is south asian H2 is more west european but also found in south asia.

http://en.wikipedia.org/wiki/Haplogroup_H_%28Y-DNA%29

Nirjhar007 said...

Mike,
''Wasn't the end of Harappan civ associated with shift of settlement to Gangetic plain?.''
Obvious Sarasvati (Modern Ghaggar-Hakra) Dried Up They had not many choices.
''we see BMAC related material appearing in Afghanistan and Indus region ...''
So the reverse, They were deep trading Neighbors,
People Try to Force Cemetery H as the ''Aryan Migration Marker'' but it has no value in practical sense whatsoever, it was at best a complex of Some Afghan Type populations and Indic ones-
http://en.wikipedia.org/wiki/Cemetery_H_culture
My Conclusion are based on the Ancient Rigvedic texts which speaks of Such Movements.

Mike Thomas said...

Nirj
Ma be you're right and I'm wrong
But read carefully what I wrote about BMAC
And it's a bit of folly to use texts written hundreds of years after the fact as "evidence " given that texts and myths are written as propaganda- stories invented to justify the rule of elite over masses ( as in anywhere and any time)

Mike Thomas said...

.. And I wouldn't take heed much the conclusions of skull shapes.. Far too crude

postneo said...

If you look at the modern distribution of H in europe there is overlap with Starcevo. I doubt this can solely be attributed to Roma.

Nirjhar007 said...

Mike,
On BMAC origins I think its from the South Caspian type Heritage nothing much Alien or Intrusive about it.
Well you should be amazed by the Accuracy of Ancient texts and its application in the case of Archaeology here a very important research on Indian Tradition-
http://www.academia.edu/7683313/The_Chronology_of_Puranic_Kings_and_Rigvedic_Rishis_in_Comparison_with_the_Phases_of_the_Sindhu_Sarasvati_Civilization
About Skull Shapes yes that's a factor but again it can suggest movements of course.

Mike Thomas said...

That's what I'm saying BMAC is "native South caspian" - as you put it .
But it did move into Indus .

Nirj, I'd have thought using the RV is about as scientific as using the bible . Archaeology and palaeoanthropological study should operate independently

Nirjhar007 said...

Mike,
''But it did move into Indus .''
Again How? there were only trade like relations it seems no Structural Type Trail or Invasive patterns, Both Just Not BMAC were heavily Influenced from and i dare say probably has origins from the Zarzian-Zagros horizons tradition! those cultures were Sisters from same heritage and not originators of one or the other though IVC is older and more Grand and confluences existed between them.
Its just not RV there are many others see that research if it helps you in some way:).

spagetiMeatball said...

David how does the Keyser 2009 study hold up in light of recent studies.

Remember the STR-matches of ancient south siberians there was a huge gap between northeastern europe and some few samples in western mongolia or something.

But we see large yamnaya ancestry in central asia and south central asia. So was that poor sampling or what?

Mike Thomas said...

Nirj

Who said Im advocating intrusion or invasions ?

Id be careful with making broad brush statements like 'sister civilizations'. Identity, language and culture work on a far more multifaceted level.

But i wholly agree, the entire region of central Asia and NW India is in dire need of attention from a more sophisticated and interdisciplinary 21st century lens. Surely young scholars form India , now that it is coming of age, can afford some attention to this, (sans an automatically AIT stance ?

Nirjhar007 said...

Mike,
Again you are quite right!
''sans an automatically AIT stance ?''
Uh if i understand correctly yes Indology for over 200 years in Academia has been observed on the basis of AIT scenario no exception , its like creating something (a THEORY) first and then to put reasoning after reasoning to support it and not giving any ground to the Other possibilities but now it seems the wheels are bit turning with new age thinkers though unfortunately not many.
The guys paper i gave is one of the promising ones...
But in a general sense taking the Question of PIE i think quite soon a major turnover is coming...

Alberto said...

I agree with ASI being a very basal component probably to all Out of Africa populations. The older the genomes we get, the more South Asian they show in admixture tests (MA-1 quite clearly, but even more Ust'-Ishim).

Balaji, do you have f3 stats involving ust'-Ishim instead of MA-1? My guess would be that if Ust'-Ishim is used, then probably more South Asian populations (like Sakilli, Chamar...) might give more negative stats with Yoruba (but I've never seen it, so it's just a guess).

ANE most likely evolved from ASI throughout the Upper Paleolithic, but whether South Asian admixture in Central Asian populations (or Yamnaya) is due to this ancestral origin or to more recent contacts is difficult to say.

Nirjhar, Mike, when referring to AIT, what's the definition of Aryan? If it refers to populations original from Northern and Eastern Europe it's one thing. But if Aryans refer to people that have been around the south Caspian, south Turkmenistan, north Afghanistan, South East Uzbekistan, Tajikistan, Kyrgyzstan,... since Mesolithic times it's a different one.

Nirjhar, what is your opinion about the origin of modern people from Pakistan (and North India)? Do you think they're native to that land or they received a migration from Iran/S-C Asia at some point?

Nirjhar007 said...

Alberto,
'' what's the definition of Aryan?''
Its Complicated:)-
http://koenraadelst.blogspot.in/2015/03/the-indo-european-vedic-and-post-vedic.html

''what is your opinion about the origin of modern people from Pakistan (and North India)? Do you think they're native to that land or they received a migration from Iran/S-C Asia at some point?''
Well Al I think India-Pak area was a large population from pre-historic period and it do show good Archaeological and cultural continuity, Archaeology Do Confirm of West-Asian Type people penetrated the Sindhu Basin during the 4500-4000 BC period in large numbers! i would like to relate those people to Proto-Indo-Europeans Coming from S Caspian and Neighboring Central Asian Area.
After That there were no ''culture changing migrations'' up to ~6oo BC period when Iranians Intruded starting a list of Numerous Migrations from Out Side from across Eurasia....

Mike Thomas said...

@ Alberto

"hen referring to AIT, what's the definition of Aryan? If it refers to populations original from Northern and Eastern Europe it's one thing. But if Aryans refer to people that have been around the south Caspian, south Turkmenistan, north Afghanistan, South East Uzbekistan, Tajikistan, Kyrgyzstan,... since Mesolithic times it's a different one"

Im not so much caught up in those rigid definitions which have dominated so far.

Whilst I cannot claim any expertise on the archaeology of central asia, to me, the age of Indo-Aryan- as currently constructed, is too young for Nirjhar's idea of a Late Neolithic time span.

But I certainly agree in other respects: the longevity of interaction, trade, and secondary movements across Middle Asia (west - east) which antedate and override any north -south, or south north movements.

But there is a link to the steppe, but it is not how it has been traditionally reconstructed.....

And Nirj, sorry i missed type before. I wanted to write that I'd hope young scholars working in India do not automatically fall to an OOI scenario.

Davidski said...

sM,

The resolution and sampling in the Keyser paper wasn't all that great.

When properly tested, the Andronovo R1a should turn out R1a-Z93, like the ancient Altai samples from Hollard et al., and ancestral to South Asian R1a-Z93.

Nirjhar007 said...

Mike,
'' India do not automatically fall to an OOI scenario.''
No the basic logical trend is to connect the Mehrgarh- SSC/IVC to Indo-European culture which i think is quite tenable and about OOI scenario well i at least with some others don't support it any longer as it neglects to describe Europe and West Asia etc in a quasy manner as the Steppe Theory does to describe the case of India.
''the age of Indo-Aryan- as currently constructed, is too young for Nirjhar's idea of a Late Neolithic time span. ''
SC Asia harbored variable IE dialects and Sanskrit has only able to preserve some part of it at best there is no need to have this idea that The Sanskrit Presence=IE Presence in the subcontinent, Same goes to Avestan of Central Asian Area.

Nirjhar007 said...

David,
''Andronovo R1a should turn out R1a-Z93, like the ancient Altai samples from Hollard et al., and ancestral to South Asian R1a-Z93.''
No sir.

Alberto said...

@Nirjhar

"Archaeology Do Confirm of West-Asian Type people penetrated the Sindhu Basin during the 4500-4000 BC period in large numbers!"

Do you have any reference to this? To me it also seems a bit too early in time.

@Mike

"But I certainly agree in other respects: the longevity of interaction, trade, and secondary movements across Middle Asia (west - east) which antedate and override any north -south, or south north movements."

Yes, agreed. The problem is that without genetic evidence it's not always easy to establish what represents cultural interaction and what represents a migration of people. That's why ancient DNA is so much needed in all this region.

Nirjhar007 said...

@Alberto
http://books.google.co.in/books/about/God_apes_and_Fossil_Men.html?id=W6zQHNavWlsC

Nirjhar007 said...

@Alberto
''Yes, agreed. The problem is that without genetic evidence it's not always easy to establish what represents cultural interaction and what represents a migration of people. That's why ancient DNA is so much needed in all this region.''
Exactly and about dating PIE i think ''PIE'' had importance to Farming+Herding but there are tons of variables to consider so its almost impossible to stamp any specific identity and age...
But contradicting Mike I favor the Transition from Neolithic-Chalcolithic period but i'm not staunch of it:).

Nirjhar007 said...

@Guys
Ancient mtDNA from cis-Baikal area
http://dienekes.blogspot.in/2015/03/ancient-mtdna-from-cis-baikal-area.html
''This paper presents the results of a study of a mitochondrial DNA sample (N = 15) from the remains of representatives of the Neolithic and Early Bronze Age (VI–III millennia BC) Cisbaikalian human population. It was found that the mitochondrial gene pool of the ancient population under study contains lineages of East Eurasian haplogroups D, G2a C, Z, and F1b. The results of the comparative analysis of the group under study with ancient and modern Eurasian populations suggest that the development of autochtonous East Eurasian genetic components was the main mechanism of the formation of the population of the Baikal region. Genetic contacts with populations of neighboring regions of Central Asia also contributed to the formation of the gene pool of the Cisbaikalian population. ''

Mike Thomas said...

Dave
I don;t think I saw "CO1" (Gamba) in your K15s. Whenever you have a spare moment, do you think you can include it ?

Thanks

Davidski said...

Here you go...

HungaryGamba_CA CO1

North_Sea 1.33
Atlantic 31.99
Baltic 2.1
Eastern_Euro 0
West_Med 46.86
West_Asian 0
East_Med 17.5
Red_Sea 0.22
South_Asian 0
Southeast_Asian 0
Siberian 0
Amerindian 0
Oceanian 0
Northeast_African 0
Sub-Saharan 0

Mike Thomas said...

Thanks David, I appreciate it.

CO1 is very Neolithic indeed.

I think the overall picture in Bronze Age Europe appears complex. IMO, its clear that it is not a case of solely migrations from east of the Dniester causing this.

I think the paper by Bollongino, Burger et al (2013), and what we otherwise know about the relative demise of early Neolithic strategy, is one big hint.

Nirjhar007 said...

Mike,
Hi!
I have a question to be answered though it may be simple, Where did the IE Folks last reached Europe? Britain?.

Krefter said...

Anyone ever notice that the only modern Euros that are deep in the CWC/YAM/BBC-MNE-SHG/WHG triangle in a PCA are Basque, South French, North Europeans(Baltic and North sea area), and Urals.

Central(inclu. French, west-south Germans-Dutch, Swiss, Austrians, Hungarians) and South Europeans drag out of this triangle towards the Middle east.

Typical Middle Eastern Y DNA is pretty much absent in Europe outside of central-south Europe. They have a pretty strong presence in Iberia and France.

In Germany and the Netherlands there's a huge genetic divide between south-west and north ones, right around the former border of the Roman empire.

Could the southern genetic shift in Iberia, France, and western-Germanic speakers have something to do with Roman(Italian, Iberian, east Mediterranean, Middle Eastern) admixture?

A genome deep in France from before 500BC would be very useful to figuring out where the east Mediterranean-type ancestry is coming from.

Mike Thomas said...

@ Nirj

Sadly I don't have a time machine :)
But if I had to hypothesize Id say Britain , Scandinavia , the baltic . ..

Krefter

Odd question .
It depends how you look at it. Ultimately, all europeans are from the "Middle East", even those with some 50% Yamnaya ancestry
As of recent ME input ; it actually appears to be rather scarce (except pockets in iberia , southern Italy and Crete).

Nirjhar007 said...

Thx Mike:).

Krefter said...

Mike, recent ME ancestry in Europe doesn't look scarce.

Italians and Balkan people are about half way between the MNE-Yamna-SHG.WHG triangle and West Asia. The affinity of these people to the Middle East may be very old, because they're geographically closer to the Middle East and there's no wall of Fire between Greece and Turkey.

Central Euros and Iberians also are outside of the MNE-Steppe-SHG/WHG triangle and slope towards west Asia. Everyone from west Germans to Portuguese. Also, British today are more southern genetically than Iron age and Medieval British.

Typical Middle Eastern Y DNA haplogroups which haven't been found or were rare in Neolithic Europeans are popular today in southeast Europe, Iberia, and France. They're a near non-existent in north Europe and Basque, but have a presence in central Europe.

Rome, Greek traders, Phoenicians, etc. I don't know may have something to do with this.

Krefter said...

Mike, someone who read Wikpedia for 30 minutes would know IEs were in Scandinavia and the Baltic as far back as 4,000YBP with Corded ware. IEs inhabited Scandinavia all through the Bronze age and migrated south in the Iron age as the Germans.

R1b-L11(west) and R1a-Z282(east) the two mega bronze age lineages of Europe both (prob.) came from the steppe with (prob.)IEs. They're border is right around the political border of Germany and Poland, no surprise. Scandinavians paternally are split between east and west IEs. A good guess is because first Corded ware was there and then Beaker and others.

Mike Thomas said...

Yes Krefter
I can tell you get your information from wikipedia ; but let's not debate about what we (think) we know or don't know about the supposed expansion of IE in northern bronze age europe

But out of interest , which "Middle Eastern" Y haplogroups are found in Central Europe ?

Mike Thomas said...

R1b and R1a

"They're border is right around the political border of Germany and Poland, no surprise. "

Yes those Bronze Age Indo europeans back in 4000 BC signed a UN brokered agreement as to which parts of Central -Northern Europe to invade and settle

Btw it's "their", not "they're"

Krefter said...

Mike,

I'm agreeing with what most experts say. That's what's on Wikipedia. Of course I consider other theories, but see less convincing evidence for them so far.

"But out of interest , which "Middle Eastern" Y haplogroups are found in Central Europe ?"

My knowledge on this is very nubby. In the next several months though I should have some new files on Y DNA. I know off of Eupedia that J and E1b in central-north Europe resemble the Roman empire in distribution.

The fact that J is absent in Neolithic Euro Y DNA, and popular in Mediterranean Europe today and has pa presence in central Europe should raise some eye brows.

Krefter said...

@Mike,
"Yes those Bronze Age Indo europeans back in 4000 BC signed a UN brokered agreement as to which parts of Central -Northern Europe to invade and settle "

Simply put: Poles descend from Corded ware and Germans partly descend from Bell beaker.

The divide between R1b-L11 dominated western IEs and R1a-Z282 dominated eastern IEs is at Germany and Poland today. For the past 4,000 years that's the border has been in that area. We can see it with 3/3 R1b in Beaker and 3/3 R1a with Corded ware.

No one designed this it's just how it happened.

Krefter said...

@Mike, hold back on the insults when you don't know where someone is coming from. I just started hobby-studying a year and a half ago, and I don't have time to become an expert in linguistics and archaeology while in school. Maybe in 10 years I'll know a thing or to.

As more genetic data comes in it will only continue to support the steppe origin of IE in Europe and the genetic shift it caused.

What else can you ask for besides Haak 2015? You have not yet described or given evidence for the "complex" causes of the bronze age genetic shift.


CWC a culture believed to be of steppe origin clusters just west of Yamna, and you think they didn't come from the steppe?

Mike Thomas said...

@ Krefter

"My knowledge on this is very nubby"

There's nothing wrong with that, but if you're going to make grand claims that much of central Europe has 'middle Eastern DNA', you should have some facts to back it up. Clearly, you don't.

""E1b" and "J"

Ive already explained this earlier on. You need to be specific about which sub-haplogroups we're looking at. because sun-groups within these otherwise large and very old haplogroups are separated by thousands of years, and thus represent very different historical-demographic processes.

The predominant haplgroup E in Europe is V13. This dates to at least the Neolithic (as evident in aNDA from Spain), and likely earlier- at least in southeastern Europe. Today, it is relatively scarce in the Near East, and its closest relatives are in North-eastern Africa. It must be a very ancient Mediterranean marker which has since disappeared in the near East but survived in the Balkans. So it is neither middle eastern nor recent.

There are, on the other hand, some more recent -"Berber" type -markers which belong to wholly different sub-branches of E. They are found in small percentages in Spain, Sicily, etc. Not in the Balkans, and certainly not in central Europe.

RE: J: Same story. It is a very old clade. So you can't just look at those simple little Eupedia maps and make (faulty) conclusions. Although more studies are needed, European J2 found in up to 20% of greeks and Italians, and it is composed of differentially distributed sub-groups. One type (J2-M12) is found all the way in india, and must represent a Neolithic dispersion from the Near/ Mid East Mesopotamia.

Another (J2a-M67/ 92) is found in the Caucasus and central Italy.

The interesting thing is that the aforementioned types of J2 found in Europe are not common in modern Turks, who harbour other types of J2, as well as J1 (a "Semitic/Arabic" marker). This lends credence to what Dave's being saying, and everyone has already known for a while - the Near East is today a different place to 20000 year ago, and even 8000 years ago.

Like in E, the more 'Arabic' type of Hg J is not at all common in modern Europeans, with the exception of the odd Gaguzian, Spaniard or Albanian.

"The fact that J is absent in Neolithic Euro Y DNA, "

Well, this is coming from a n=o studies from Italy and the Balkans, and a handful of samples from Spain. Granted Neolithic central Europe was dominated by G2a, but who knows what was happening in the Mediterranean Europe (Cardial region) ? And by the Bronze age, we see J2a appearing in Hungary (BR2 in Gamba).


"I know off of Eupedia that J and E1b in central-north Europe resemble the Roman empire in distribution. "

Possibly contributed. But, so , how is this "Middle Eastern" ? Last time I checked Rome and Italy were in Europe

Krefter said...

Mike, think about linguistics at a personal family level. How the hell could language not be all about genetics? We learn our first language in our homes and small closely related communities. This was even more true in the past.

Before large states like Rome, it would have been difficult for the elitist to force everyone to speak their language.

Language and genetics were clearly one and the same to CWC tribes.

The same steppe-genes are abundant and in some cases dominate in modern IE Euros because IE speech has been passed down through family, not elitist.


The same goes for the spread of farming in Europe. Two key events the "elitist and spread of ideas" crowd which was mainstream has been proven wrong in.

Balaji said...

Alberto,

You had written, “I agree with ASI being a very basal component probably to all Out of Africa populations. The older the genomes we get, the more South Asian they show in admixture tests (MA-1 quite clearly, but even more Ust'-Ishim)."

I don't think ASI is in all Out-of-Africa populations. Early and Middle Neolothic Europeans did not have it and neither do present-day Basques or Sardinians. For this, I am going by the presence of absence of the purple component at K=6 in the ADMIXTURE figure of Haak (link below). This component that is modal in Papuans, I am treating as a proxy for ASI.

http://biorxiv.org/content/biorxiv/suppl/2015/02/10/013433.DC1/013433-1.pdf

South-Easterrn Europeans such as Greeks, Albanians, Tuscans, Bergama, Bulgarians, Maltese, Sicilians etc have more of this component than do Northern Europeans. This suggests that Southern Europe had an influx of people from a different route at around the same time that Central Europe was experiencing migration from the steppe.

Davidski provided the following f3 stats.

Germany_MN Papuan Greek -0.00282 0.001039 -2.713
Germany_MN Papuan Sicilian -0.002636 0.001078 -2.445
Germany_MN Papuan Tuscan -0.001725 0.001172 -1.472
Germany_MN Papuan Bulgarian -0.003126 0.001125 -2.778
Germany_MN Papuan Croatian -0.000567 0.001108 -0.511

The f3 stats for the above South-Eastern European populations are all negative. The z values do not quite reach 3. But since there are several such populations, together I think they reach statistical significance indicating that present-day South-Eastern Europeans do have some Papuan-like ancestry

Alberto, I remember reading your suggestion that ANE might have entered Southern Europe by a different route than in Northern Europe. This is also supported by analysis of mtDNA in a paper discussed by Davidski in his latest post.

Kristiina said...

Thank you for your link Nirjhar!

Personally, I prefer the idea that Uralic and IE languages share a language among their ancestor languages as I believe in mixing of genes as well as languages. As long as things are not proven, we can stick to our pet theories, and I also know that many will stick to theirs also after that. :-) At the moment, OIT is in big difficulties; Central Asian -centred theories are, however, doing better. On the other hand, I admit that Davidski also has his point. I am really waiting for new linguistics and genetic insights.

I am very interested in your linguistic work as I have my own linguistic project under way as well. So, I am sure we could benefit from our special focus areas.

Kota means a kind of yurta in Finnish. It is found in almost all Uralic languages with small semantic variations. A similar word is also found in Turkic and Mongolic languages and Ainu in the meaning of village. In selkup ”kette” means fence. I am not so sure about Sishu... Sisu means ”perseverance”, and it comes from a word meaning ”inside”. What does it mean for you?

Cheers…

Nirjhar007 said...

Kristiina,
Nope I don't prefer OIT but South Of Caspian though the researcher i linked does.
Yes there are very important aDNA studies coming up we can consider ourselves lucky to live in this age actually.
Yes at the moment i'm working with Prof. Benedetti to establish a good research on PIE borrowings in different Non-IE languages and the reverse with some thought on structural similarities also, a related post will appear in few days and i will inform you BTW what are you up to? if you can tell in a general sense of course:).
Kota's meaning is then similar to Sanskrit meaning dwelling,hut,shade,strong hold,fort etc But sadly Sishu is probably not as it means ''Child'' in Sanskrit and in Various IE dialects of India,
The Thing is that the 2 are alleged to to be of ''Dravidian Donation'' to Indo-Aryan and they also appear in Uralic though the second one with different meaning as it appears....
Cheers.

Nick Patterson (Broad) said...

@Balaji

A technical comment:
Beware of the "outgroup case"
This is discussed in my
"Ancient Admixture" paper.
Note that modern European pops
all are admixed with MNeolithic
and ANE; so this is especially
plausible.
That is your negative Z scores are
(I think) to be expected.
I'd like to think about formal testing for ASI in Europe.
Don't know how to do that!

Nick

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