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Monday, February 6, 2017

No game changer


I had a quick look at how the new ancient samples from the East Baltic and Pontic Steppe affect the current models of the peopling of Northern and Eastern Europe. I did this with a series of qpAdm runs.

Outgroups
AG3-MA1
Barcin_Neolithic
Chukchi
Dusun
Igorot
Iran_Neolithic
Karitiana
Kosipe
Kostenki14
Lebbo
Levant_Neolithic
Mbuti
Ust_Ishim
Villabruna

Latvian
Caucasus_HG 0
Latvia_HG 0.270
Latvia_LN1 0.493
Lengyel_LN 0.237
chisq 5.054 tail_prob 0.928542

Latvian
Caucasus_HG 0
Latvia_HG 0.240
Lengyel_LN 0.291
Yamnaya_Samara 0.470
chisq 6.092 tail_prob 0.867148

Lithuanian
Caucasus_HG 0
Latvia_HG 0.253
Latvia_LN1 0.502
Lengyel_LN 0.245
chisq 3.609 tail_prob 0.980002

Lithuanian
Caucasus_HG 0
Latvia_HG 0.212
Lengyel_LN 0.338
Yamnaya_Samara 0.450
chisq 9.633 tail_prob 0.56368

Polish
Caucasus_HG 0
Latvia_HG 0.216
Latvia_LN1 0.444
Lengyel_LN 0.340
chisq 5.285 tail_prob 0.916602

Polish
Caucasus_HG 0
Latvia_HG 0.136
Lengyel_LN 0.397
Yamnaya_Samara 0.466
chisq 11.457 tail_prob 0.405777

Scottish
Caucasus_HG 0
Latvia_HG 0.167
Latvia_LN1 0.433
Lengyel_LN 0.399
chisq 6.746 tail_prob 0.819232

Scottish
Caucasus_HG 0.066
Latvia_HG 0.153
Lengyel_LN 0.403
Yamnaya_Samara 0.379
chisq 6.166 tail_prob 0.801147

Swedish
Caucasus_HG 0
Latvia_HG 0.219
Latvia_LN1 0.437
Lengyel_LN 0.344
chisq 6.648 tail_prob 0.826865

Swedish
Caucasus_HG 0
Latvia_HG 0.147
Lengyel_LN 0.394
Yamnaya_Samara 0.459
chisq 7.207 tail_prob 0.782122

...

Latvia_LN1
Caucasus_HG 0.399
Eastern_HG 0.448
Lengyel_LN 0.137
Nganasan 0.016
chisq 4.997 tail_prob 0.891348

Yamnaya_Samara
Caucasus_HG 0.381
Eastern_HG 0.507
Lengyel_LN 0.112
Nganasan 0
chisq 14.138 tail_prob 0.225426

All of the models above had fairly reasonable standard errors, and despite the fact that the analyses featuring Latvia LN1 were based on just ~8K SNPs, I can confidently say that these new samples are hardly a game changer by any stretch. Here's what I learned:

- Latvia LN1 or Latvian Corded Ware is basically interchangeable with Yamnaya as the main source of "eastern" ancestry in Northern and Eastern Europe, supporting the conclusion in Jones et al. that Latvia LN1 was of steppe origin, and the current consensus that modern-day Northern and Eastern Europeans derive a large part of their ancestry from the Early Bronze Age steppe

- Latvia HG is more or less interchangeable with Western HG as the main source of extra forager ancestry in Northern and Eastern Europe, and despite its inflated Eastern HG ancestry relative to Western HG, it doesn't have a big impact on the estimates of steppe ancestry across Northern and Eastern Europe

- Nganasan from Siberia are not necessary to obtain tight fits for many Northern and Eastern Europeans in models including Latvia LN1, possibly due to low level Nganasan-related ancestry in this ancient sample (although that's really tough to check properly at the moment with the low number of markers on offer)

- the Eastern HG-like Latvia MN2 appears to be irrelevant to the population history of much of Northern and Eastern Europe, for the most part because it's not a more parsimonious solution to the origins of Eastern HG-related ancestry in most of Europe today compared to the Yamnaya-like steppe pastoralists (and that's because we'd need an expansion of basically unadmixed Caucasus Hunter-Gatherers across the northern half of Europe, and they're not present anywhere in the already ample Eastern and North-Central European ancient DNA record). Moreover, I'm unable to successfully model Latvia LN1 as part Latvia MN2, although that might be because of only ~5K SNPs available for the test.

Citation...

Jones at al., The Neolithic Transition in the Baltic Was Not Driven by Admixture with Early European Farmers, Current Biology, Published Online: February 02, 2017, DOI: http://dx.doi.org/10.1016/j.cub.2016.12.060

See also...

First look at Latvian and Ukrainian ancient genomes

qpAdm tour of Europe: the Bronze Age invasion

126 comments:

Simon said...

Can it be inferred from the Lengyel scores in Yamnaya_Samara and Latvia_LN1 that the EBA Steppe people had minor admixture from EEF? It would make sense from a linguistic and archaeological POV insofar as the Proto-Indo-Europeans traded with the sedentary peoples of Central/Eastern Europe and got their cattle originally from them (*tawr).

Antoni Małkowski said...

https://aleximreh.wordpress.com/2017/02/01/daci-geti-goti-n-europa/
Czy ten artykuł ma racje bytu? Jest bardzo sugestywny.

Romulus said...

@Antoni

You made such a nice map too bad it's completely wrong. Awwww.

Karl_K said...

This is exactly why I haven't commented for months. No game changers. Boring stuff really.

When are we gonna see some of these more exciting and interesting results?

Matt said...

All a bit disappointing. There's got to be more structure to explain beyond the simple Europe_EN+Yamnaya+extra WHG model (even the qpAdm models don't quite recapitulate the right tree and plot shapes for modern people), but this new data doesn't really seem to add anything useful to that.

@Davidski, just for something to do with the new data could you test these D-stats btw?

Mbuti Kotias Yamnaya_Samara Latvia_LN1
Mbuti Kotias EHG Latvia_LN1
Mbuti Kotias Ukraine_HG Latvia_LN1
Mbuti Kotias Latvia_HG Latvia_LN1
Mbuti Kotias Latvia_HG Yamnaya_Samara
Mbuti Kotias Ukraine_HG Yamnaya_Samara
Mbuti Kotias EHG Yamnaya_Samara
Mbuti EHG Yamnaya_Samara Latvia_LN1
Mbuti Ukraine_HG Yamnaya_Samara Latvia_LN1
Mbuti Latvia_HG Yamnaya_Samara Latvia_LN1
Mbuti Corded_Ware_Germany Yamnaya Latvia_LN1
Mbuti Corded_Ware_Estonia Yamnaya Latvia_LN1
Mbuti Corded_Ware_Poland Yamnaya Latvia_LN1
Mbuti Bell_Beaker_Germany Yamnaya Latvia_LN1

Alberto said...

To me the models look good, especially much improved for Lithuanian with these samples (same as with PCA data), without Yamnaya_Samara there. All except the model for Latvia_LN1. It seems that again qpAdm can't see well the difference between EHG and WHG. The best match for Latvia_LN would be Ukraine_HG (because Ukraine_N1 has Papuan-like noise and is a bad source that no one picks) or even Latvia_HG. So something SHG-like. Which would explain everything else quite nicely (stats-wise).

Could be tested with this stat to check how correct that model is:

Yamnaya_Samara Latvia_LN1 Eastern_HG WHG

Roy King said...

Open Genomes Foundation noticed from Genetiker that Latvia_MN1 is derived for a M269 SNP but ancestral for 13 M269 SNPs. We were speculating that M269 may have originate in NE Europe (Baltic to Samara) and spread southward to Anatolia/Yamnaya and ultimately westward to France and Iberia. M73 is just parallel geographically to the M269*. OGF also reported Rise098 from South Sweden is a true U106* geographically nearby.

Romulus said...

https://www.youtube.com/watch?v=rSjK2Oqrgic

Ryan said...

Even if it's expected I think confirmation that existing assumptions were correct is always worthwhile.

It seems like the fits using Latvian HG are generally better than those using Yamnaya. Is that in line with earlier expectations that the true root of the Indo-European tree lies with a population with a bit more WHG-like ancestry rather than just EHG with Yamnaya? Does Latvian HG give a better fit for more eastern populations?

Roy King said...

There is also the notion that the Baltic languages are the most conservative of the IE languages and maybe lacked much of a pre-IE substrate.

Rob said...

@ Roy

We're did Terry note this ?

Matt said...

Also, re the main thread, how do models of CHG, Ukraine_N1, Latvia_LN1 / Yamnaya, Lengyel_LN function, if at all (and there is enough overlap to test them)?

Another question, how do Ukraine_N1 and Latvia_HG function for Lengyel_LN as admixing with Barcin_N? Same for Esperstedt and Baalberge and Iberia_Chal if possible. I'm interested in whether either of them are plausible sources for admixture in those populations, and whether the Lengyel sample is recognisably local HG + Barcin or is not distinguishable from Loschbour / La Brana + Barcin. Latvia_HG looks a little different in its selective SNPs from Loschbour / La Brana (some presence of SLC24A5) and Ukraine HG is quite different so there could be some potential to set up a varying selective pattern, if nothing else.

Davidski said...

@Matt

Lack of power in a lot of these.

Mbuti Caucasus_HG Yamnaya_Samara Latvia_LN -0.0094 -0.71 20942
Mbuti Caucasus_HG Eastern_HG Latvia_LN 0.0154 0.927 19805
Mbuti Caucasus_HG Ukraine_HG Latvia_LN 0.0405 1.254 5986
Mbuti Caucasus_HG Latvia_HG Latvia_LN 0.0127 0.825 20992
Mbuti Caucasus_HG Latvia_HG Yamnaya_Samara 0.0257 4.793 108885
Mbuti Caucasus_HG Ukraine_HG Yamnaya_Samara 0.0266 2.336 30026
Mbuti Caucasus_HG Eastern_HG Yamnaya_Samara 0.0263 7.929 1025675
Mbuti Eastern_HG Yamnaya_Samara Latvia_LN 0.0088 0.567 19687
Mbuti Ukraine_HG Yamnaya_Samara Latvia_LN 0.0207 0.713 5942
Mbuti Latvia_HG Yamnaya_Samara Latvia_LN 0.0103 0.776 20844
Mbuti Corded_Ware_Germany Yamnaya_Samara Latvia_LN -0.0029 -0.248 20791
Mbuti Corded_Ware_Estonia Yamnaya_Samara Latvia_LN -0.0043 -0.225 11834
Mbuti Corded_Ware_Poland Yamnaya_Samara Latvia_LN 0.0543 1.18 2274
Mbuti Bell_Beaker_Germany Yamnaya_Samara Latvia_LN 0.0101 0.937 20743

@Alberto

Yamnaya_Samara Latvia_LN Eastern_HG Western_HG -0.0018 -0.113 19686

Matt said...

Wow, no kidding, low power. I guess that's why there wasn't any test of any of this stuff in the paper.

Rob said...

David
Your models for N and W Europeans which include Latvia LN might be redundant - if they already contain Latvia HG and Kotias.
Extra EHG is probably by way of local admixture with slightly more EHG shifted women which were alteady present in Baltic Or picked up on the steppe

Samuel Andrews said...

@Davidski,

Can you test if UkraineHG/N replace EasternHG as the EuroHG ancestor of Yamnaya and LatvianLN? Can you then test if they perfer EasternHG or UkraineHG/N by including both as ancestors?

Also can you put HungaryBA, IrishBA, and PolishEBA through the same tests you put modern pops in?

Alberto said...

@Davidski

Thanks. Yes, quite underwhelming stats. Nothing to do with qpAdm itself. That one you run for me doesn't seem to agree with either the PCA data or the Admixture data (form Basal-rich K7). No wonder it was difficult to know fine details from formal stats about these samples.

Angantyr said...

Isn't Latvia_MN2 the first sample of Comb Ceramic autosomal DNA that has been published? As such, few would assume that it had much impact on IE speakers.

But - at least once upon a time - some people used to believe that the Comb Ceramic culture were early Uralic speakers. So it could be interesting to see if any current Uralic speakers show any preference for Latvia_MN2.

JohnHutchins12 said...

Yes, I would have also expected Latvia_MN2 to be N1c instead of R1b if he was Comb Ceramic.

Samuel Andrews said...

Latvia_MN2 didn't receive a Y DNA result. I think she might be female. Latvia_MN1, who was like Latvia_HG genetically, had R1b.

JohnHutchins12 said...

That makes sense then. I was going off of what someone said in another forum.

Davidski said...

@Simon

Yamnaya does have some sort of minor Anatolia Neolithic-derived admixture that often doesn't show up in ADMIXTURE runs, but does show up in formal models. It might be from Cucuteni-Tripolye and/or Varna, or from the earlier Balkan farmers described in that recent Mathieson et al. ASHG abstract. I use Lengyel LN as a stand in for now, because it seems to produce the best results across the board for ancient and modern Europeans.

@Karl

Yes, but there won't be any game changers. Most of us are just waiting for the details and closure, and of course a lot of awesome samples.

@Ryan

I think you mean Latvia LN. Yes, it seems to be a better reference than Yamnaya Samara for Eastern Europeans, but I haven't tested any Uralic or outlier populations yet. I also haven't tested most Western and Southern Europeans.

@Roy

Apparently there is non-IE substrata in the Baltics. Only place where it doesn't exist is Southern Russia. See here...

http://www.youtube.com/watch?v=vFZhWfL0ocY&list=PLAXoDomeFLX90fTHi0W8lYBtEoZHSBH2i&index=13

@Samuel

Can't test most of that stuff right now. Too difficult. But I can show you the models for Hungary BA.

Hungary_BA
Caucasus_HG 0
Latvia_HG 0.317
Latvia_LN 0.049
Lengyel_LN 0.634
chisq 12.843 tail_prob 0.303704

Hungary_BA
Caucasus_HG 0
Latvia_HG 0.306
Lengyel_LN 0.642
Yamnaya_Samara 0.052
chisq 13.629 tail_prob 0.254202

@Angantyr

I haven't tested any modern populations yet with Latvia MN2, for the reasons described in the post. But I can imagine it might be a decent reference for a lot of European groups, simply because it resembles Eastern HG so much.

At some point I'll try and test whether it has Nganasan-related ancestry, and also how it performs in models for Northeast European Uralics.

Samuel Andrews said...

@Davidski,

Thanks! Can you do the same test for Basque that you did for HungaryBA. I think what differntaies the two is Basque's ANE is from the Steppe while HungaryBA's ANE is from Eastern European hunter gatherers like UkraineHG.

Chad Rohlfsen said...

Best Beaker fits require Ukraine HG in good amounts.

Olympus Mons said...

@Chad
The is no BB dna. So does not require anything.
Germany sample were half breeds between CWC and BB.

When we have REAL Bell beakers then we will see.

Rob said...

Dave
Can you comment as to why you're so desperate to somehow make EHG relevant ?

Davidski said...

@Samuel

Sure, but let's keep this from Maju.

Basque_French
Latvia_HG 0.187
Latvia_LN 0.270
Lengyel_LN 0.543
chisq 3.961 tail_prob 0.971054

Basque_French
Latvia_LN 0.302
Lengyel_LN 0.543
Western_HG 0.155
chisq 3.869 tail_prob 0.973581

Basque_French
Latvia_HG 0.140
Lengyel_LN 0.595
Yamnaya_Samara 0.264
chisq 5.474 tail_prob 0.906043

Basque_French
Lengyel_LN 0.563
Western_HG 0.082
Yamnaya_Samara 0.355
chisq 15.364 tail_prob 0.166411

Davidski said...

@Rob

Can you comment as to why you're so desperate to somehow make EHG relevant?

Because it is relevant. You should know this, because you've been reading the same ancient DNA papers as me.

The only way it will become less relevant, is if it turns out that it's just a proxy for what is really Ukraine HG in Corded Ware, most of Yamnaya, and thus modern day Europe. But so what, since EHG and Ukraine HG are basically the same thing.

You can't make the Latvian HG and MN samples the source of EHG ancestry in Corded Ware and modern-day Northern/Eastern Europe because for one, you'd need pure Caucasus Hunter-Gatherers to be living in Northern/Eastern Europe. But they're not there, and it's highly unlikely that anyone will find them there.

Rob said...

Davidski
It's called migration from Majkop
Between Majkop (whom I predict will be 75% CHG & 25% EHG) and the (sometimes amply) EHG infused locals in Ukraine and Poland, there is ample ANE to satisfy the early models' requirements for ANE. This Samara EHG falls into irrelevance for all but Yamnaya itself.

Samuel Andrews said...

@Rob,

Think about it. You and Maju claim we just haven't found the aDNA prove your hypothesis are correct but will find that aDNA in the future. In contrast there is actual aDNA prove people basically identical to Yamnaya Samara lived deep deep in Europe, as far west as Germany.

Why argue the EHG-type and CHG-type ancestors of Europeans mixing in Eastern Europe instead of Russia. Why complicate things?

Also Rob even if your hypothesis is correct most of Europe received migration from people similar to Corded Ware. This is because most of Europe isn't Eastern Europe. Most of Europe wasn't inhabited and never was inhabited by UkrainHG or EHG or even LatvainHG types. The hunter gatherers of Western Europe had already been absorbed by farmers by 3000 BC. So Irish for example are definitly not a mixture of Maikop, EEF, and Irish HGs.

Davidski said...

@Rob

It's called migration from Majkop.

There's no evidence of this migration with the data that is available. Most reasonable people here will back me up on that.

You obviously believe that this evidence will come, and you're free to do that, I'm not stopping you. But I don't, and I'd rather base my views on the already ample data from Eastern Europe that we have available.

Samuel Andrews said...

@Rob,
"If you are going to attempt to reply to me, then pass elementary school first, because it seems you haven't yet acquired the ability to read"

I did reply to you! Saying I didn't reply to you won't allow you to cope out of our argument.

"The mixing for Proto BB and CWC took place in EE not Russia"

How do you know this? Like with your overall hypothesis, that isn't supported by aDNA.

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

Population, Iran_Neolithic:I1945, Chamar, Ukraine_N1:StPet12, X, D statistic
Brahmin___, 27, 57, 16, 0, 0.0053
Brahmin_TN, 24, 67, 9, 0, 0.0033
Brahmin_UP, 23, 62, 15, 0, 0.0044
GujaratiA__, 31, 52, 17, 0, 0.0061
GujaratiB__, 28, 57, 15, 0, 0.0056
GujaratiC__, 23, 69, 8, 0, 0.0043
GujaratiD__, 18, 78, 4, 0, 0.0039
Kshatriya__, 23, 65, 12, 0, 0.0043

Ryan said...

@David - You're right. I'd be interested in seeing how it compares to steppe cultures from Central Asia to see if this is closer to the root of everything or just western IE.

Chad Rohlfsen said...

Why would Maykop be 75% CHG and 25% EHG, when Armenian CA samples are quite Anatolian shifted? mtDNA doesn't look like CHG plus EHG either.

Davidski said...

@Rob

Already ample data from Majkop?

I'm not sure how data from Majkop will help you unless Majkop samples look very similar to Yamnaya and Latvia LN, and carry M269 and/or M417.

I can't see that happening at this stage of the game. But maybe that's just me.

Your theory has always been that the pastoralists can't have come from further west than Samara is crashing down.

Can you show me where I said that?

I repeatedly said that Corded Ware came from the steppe, probably from somewhere around the Volga or Don. Those comments are still in the comments section here and blog posts.

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

http://eurogenes.blogspot.com.au/2015/06/101-ancient-eurasian-genomes-allentoft.html

Davidski said...

Rob, spot the difference...

You claim I said this: Your theory has always been that the pastoralists can't have come from further west than Samara.

As per the quote you dug up, I said this: The question is whether both (CWC and Yamnaya) derive from the same population, like Khvalynsk and related groups from around the Volga and Don. The answer is yes.

The Don is a fair way west of the Samara, no?

You also boasted that there won't be any R1 or EHG type admixture west of Khvalysnk.

You mean like when I talked about Sredny Stog from WEST of Khvalynsk potentially harboring populations rich in EHG and R1a? Sure, OK.

Arza said...

Population,Kotias:KK1,Latvia_MN2:ZVEJ31,X,X,D statistic
Yamnaya_Kalmykia:RISE240,43,57,0,0,0.0098
Yamnaya_Kalmykia:RISE546,43,57,0,0,0.0055
Yamnaya_Kalmykia:RISE547,43,57,0,0,0.0078
Yamnaya_Kalmykia:RISE548,42,58,0,0,0.0062
Yamnaya_Kalmykia:RISE550,44,56,0,0,0.0086
Yamnaya_Kalmykia:RISE552,46,54,0,0,0.0064
Yamnaya_Samara:I0231____,43,57,0,0,0.0062
Yamnaya_Samara:I0357____,43,57,0,0,0.0128
Yamnaya_Samara:I0370____,44,56,0,0,0.0063
Yamnaya_Samara:I0429____,40,60,0,0,0.0056
Yamnaya_Samara:I0438____,42,58,0,0,0.0059
Yamnaya_Samara:I0439____,44,56,0,0,0.0059
Yamnaya_Samara:I0441____,43,57,0,0,0.0081
Yamnaya_Samara:I0443____,46,54,0,0,0.0057
Yamnaya_Samara:I0444____,40,60,0,0,0.008
Afanasievo:RISE507______,45,55,0,0,0.0122
Afanasievo:RISE508______,45,55,0,0,0.0116
Afanasievo:RISE509______,43,57,0,0,0.0072
Afanasievo:RISE510______,43,57,0,0,0.0119
Afanasievo:RISE511______,41,59,0,0,0.0087
Andronovo:RISE500 ______,36,63,0,1,0.028
Andronovo:RISE503 ______,39,60,0,1,0.03
Andronovo:RISE505 ______,36,63,0,1,0.0243
Andronovo:RISE512 ______,36,64,0,0,0.0273

Population,Kotias:KK1,Ukraine_N1:StPet12,MA1:MA1,Latvia_LN1:ZVEJ28,D statistic
Yamnaya_Kalmykia:RISE240,31,38,14,17,0.0069
Yamnaya_Kalmykia:RISE546,17,13,23,47,0.0064
Yamnaya_Kalmykia:RISE547,19,16,25,40,0.0096
Yamnaya_Kalmykia:RISE548,16,16,26,42,0.0067
Yamnaya_Kalmykia:RISE550,23,23,17,37,0.0069
Yamnaya_Kalmykia:RISE552,22,13,23,42,0.0095
Yamnaya_Samara:I0231____,16,14,25,45,0.0038
Yamnaya_Samara:I0357____,22,21,28,29,0.0149
Yamnaya_Samara:I0370____,19,15,22,44,0.0052
Yamnaya_Samara:I0429____,13,15,21,51,0.007
Yamnaya_Samara:I0438____,16,15,27,42,0.0058
Yamnaya_Samara:I0439____,24,21,24,31,0.0079
Yamnaya_Samara:I0441____,21,20,26,33,0.009
Yamnaya_Samara:I0443____,23,15,20,42,0.0057
Yamnaya_Samara:I0444____,13,16,24,47,0.0079
Afanasievo:RISE507______,21,16,11,52,0.0041
Afanasievo:RISE508______,22,19,9,50,0.004
Afanasievo:RISE509______,25,28,23,24,0.0075
Afanasievo:RISE510______,20,18,29,33,0.0102
Afanasievo:RISE511______,20,24,27,29,0.0079
Andronovo:RISE500 ______,34,63,0,3,0.0261
Andronovo:RISE503 ______,36,58,0,6,0.0284
Andronovo:RISE505 ______,32,58,2,8,0.0212
Andronovo:RISE512 ______,24,46,30,0,0.022

Davidski said...

@Rob

We've had these discussions before. This one is about Sredny Stog. No point having the same discussion all over again.

http://eurogenes.blogspot.com.au/2015/12/mixed-marriages-on-early-eneolithic.html

Davidski said...

@Arza

You need to accompany those stats with some coherent comments.

Rob said...

@ Dave
Your model demands genetic descent, or thereabouts , whereas I envisage a chain of interlinked cultures interacting from Baltic to. Black Sea and Caucasus from 4000 BC

Davidski said...

Your model demands genetic descent, or thereabouts.

And things are looking very good for my models, which aren't my models, strictly speaking, but wahtever.

So I don't need to claim any pigeon post scenarios, because I have ancient DNA evidence for the necessary migrations at the right time.

Davidski said...

Yes, from eastern Poland. Even if I'm wrong, I'll still be very close.

Arza said...

OK...

The first one - probably you don't like the idea of choosing Chamar instead of Paniya, but the problem is that Paniya don't and won't work, because this population is not situated at the end of the cline.

Here:
https://4.bp.blogspot.com/-9VulA3dYrcE/WAwe2uKQGeI/AAAAAAAAABo/gGUnbpSZXQMo9QtNOrbg1S33c3cVoAXIACLcB/s1600/4.png

...you can see 3 clines:

1. from the supposed PIIr. via Brahmin to Chamar
2. Chamar - Paniya
3. Paniya - Bonda

In certain dimensions Paniyas land behind Austroasiatic:

https://1.bp.blogspot.com/-JuNPszdTdMk/WAwe2IT6aDI/AAAAAAAAABY/w4ngYCw5ykUUJGs-uGiVQllUv5PegNC-QCLcB/s1600/14.png

As soon as you switch to Chamar scores improve significantly. And I think that there is a high chance that PIIr. have met population like them.

Also this new Ukrainian pop is a good candidate for Pre-PIIr IMHO.

The second - Yamna - I was testing some possibilities...
1. Latvia MN2 looks (at least on a PCA) like a better solution than Karelia. No Anatolian shift needed. Moreover we haven't found any R1b in Karelia yet, and we already know that some R1b was present in Latvia - maybe they've picked up few R1b HG guys there when they bounced off the Baltic shores?
2. Samples used here create a tetrahedron that more or less encloses Yamna. I wanted to check another scenario - that CWC is something like Latvia LN + farmers (shifted West), and Yamna is Latvia LN + ANE (shifted East). Theoretically it works. But Kotias/MN2 seems to be a better solution. It's simpler and provides a link to the Baltic R1b pool (even if the clades don't match, I didn't check this frankly speaking, it creates a bridge from NW to SE).

human443 said...

You need to throw an EHG into the outgroups, the most logical being the one that has the least likelihood of having any DIRECT mixture into modern populations, Yamnaya, or Latvia_LN1. That may be Karelia_HG?

Yamnaya_Samara should prefer Samara_HG or Samara_Eneolithic. And if you are correct, Latvia_LN1 should behave the same, maybe with minor local contribution, and the rest of Europe to the south and west might take a bit of Ukrainian neolithic.

Otherwise all you've concluded regarding EHG is the proportion, not the source, which I believe is the main point of contention.

Nirjhar007 said...

Since we are talking about Slavs , on which I am studying on linguistic grounds, out of curiosity , can anyone please tell me here :

1. Which Archaeological Culture(s) from which period(s) according to the current scholarship is regarded, as the originator of the Slavs, with clear and traceable Slavic motifs and materials? .

2. If any of such site(s) is genetically worked on , what the results suggest?.

I will be very grateful if anyone gives me the valid suggestions.

Davidski said...

@human443

Yamnaya_Samara should prefer Samara_HG or Samara_Eneolithic. And if you are correct, Latvia_LN1 should behave the same, maybe with minor local contribution, and the rest of Europe to the south and west might take a bit of Ukrainian neolithic.

I don't think Latvia LN1 has ancestry from Samara, but rather from the Dnieper Don region. So I'm not sure what you mean by saying "if you are correct"?

The main point I'm making is that Latvia LN1 is from the steppe. The fact that it's basically interchangeable with Yamnaya Samara in my tests proves this.

The reason it's interchangeable with Yamnaya Samara is probably because there wasn't much variation on the western steppe from the Samara to the Don, with very similar forager and farmer groups contributing to the formation of the Early Bronze Age groups there.

I don't need to put Karelia HG in the outgroups for this. I already have 14 samples there, including safer options than Karelia HG: AG3, MA1 and Villabruna.

human443 said...

@Davidski

[i]The main point I'm making is that Latvia LN1 is from the steppe. The fact that it's basically interchangeable with Yamnaya Samara in my tests proves this.[/i]

I'm not contending the idea, I'm just saying you haven't yet proven it.

The reason an EHG in the outgroups is necessary is because with your current setup, the various EHG are going to have relationship to AG3-MA1 based only upon how much ANE they have. In this case, as long as WHG and ANE are correct in proportion, any EHG will work. Does it make sense to model Yamnaya_Samara as receiving it's EHG from Latvia_MN2? Probably not, but with your current outgroups, you probably could. This could be fixed by adding and EHG to the outgroups because the EHG themselves are going to have differential relationships to each other based on proximity over time. So in this case, it could be revealed that Latvia_MN2 is not a good choice, maybe because it has too high of an affinity to Karelia_HG, versus say, Samara_HG, who may fit just right.

Seinundzeit said...

I have to agree with David here.

This debate seems to involve a fixation with highly specific spatio-temporal dynamics.

If you're into the archaeology, that stuff is obviously quite important/essential.

But, the population genetic picture remains rather unchanged, with regard to affinities and proportions.

I mean, both Yamnaya and this Latvian Corded Ware samples are the product of mixture/hybridization between EHG-related and CHG-related ancestries, with some minor Neolithic European-related admixture. Note the use of the word "related". Very important.

And, considering the interchangeability between Yamnaya and this Latvian Corded Ware sample, it's clear that Latvia_LN1 was of steppe origin. Nothing seems to have changed.

So, why was/is the debate so heated?

One almost gets the impression that a Trump staff member spiked all your drinks, with whatever the hell those guys are on. (LOL)

Anyway, (to my pleasant surprise) when using nMonte with 7 PCA dimensions, I get virtually identical results to David's qpAdm runs.

It's my "classic" (lol) setup, but with LN1 instead of Yamnaya:

Latvian

49.55% Latvia_LN1
29.80% Villabruna
18.55% LBK_EN
2.10% Ulchi

Distance=0.3717

Lithuanian

50.60% Latvia_LN1
26.15% Villabruna
21.80% LBK_EN
1.45% Ulchi

Distance=0.3402

Pretty awesome. This method is nothing like qpAdm, and my non-Latvia_LN1 references are very distinct from what David has utilized.

Yet, despite being a very different method, and despite using different references, the results are basically identical to qpAdm!

Here are South Central Asians and West Asians, using the exact same reference populations:

Kalash

51.65% Iran_Neolithic
34.50% Latvia_LN1
13.85% Bonda

Distance=1.1681

Pakistani Pashtun, tribal Areas

51.2% Iran_Neolithic
33.9% Latvia_LN1
10.4% Bonda
4.5% Ulchi

Distance=0.5571

Afghan_Pashtun, Ghilzai

50.75% Iran_Neolithic
34.65% Latvia_LN1
9.70% Bonda
3.50% Ulchi

Distance=0.4635

Pakistani Pashtun, Waziristan

39.8% Iran_Neolithic
36.3% Latvia_LN1
11.6% Iran_Chalcolithic
6.9% Bonda

Distance=0.3544

Iranian_Bandari

38.10% Iran_Neolithic
34.5% Iran_Chalcolithic
17.10% Latvia_LN1
5.2% Bonda
3.05% Levant_Neolithic
1.40% Gambian
0.65% Ulchi

Distance=0.0295


Iranian_Persian
49.05% Iran_Chalcolithic
19.95% Iran_Neolithic
13.15% LBK_EN
11.00% Latvia_LN1
3.90% Ulchi
2.25% Levant_Neolithic
0.70% Bonda

I use the Bonda, since they provide a nice upper bound estimate for ASI admixture (since they themselves are anywhere from 10% to 20% West Eurasian).

human443 said...

@ Seinundzeit

How can you say this...

"This debate seems to involve a fixation with highly specific spatio-temporal dynamics. If you're into the archaeology, that stuff is obviously quite important/essential."

And this...

"So, why was/is the debate so heated? One almost gets the impression that a Trump staff member spiked all your drinks, with whatever the hell those guys are on. (LOL)"

In this same post? That's just stupid. Important things create heated debates. Resolved uncertainties end debates.

The data is now available to answer the archaeological questions better than they have been answered prior. Why not do it?

Unless you and Davidski want people to keep proposing "an expansion of basically unadmixed Caucasus Hunter-Gatherers across the northern half of Europe" which they have every right to with the current analysis. How does one strip that right and reinforce the ideas that Davidski has proposed? Show that the EHG transmitted via steppe expansions comes predominantly from one place neighboring the CHG homelands that could support a steady CHG introgression over time rather than a major independent CHG migration.

Davidski said...

@human443

I'm just saying you haven't yet proven it.

Really not sure why you're saying that, since, like I said, Latvia LN1 is very much interchangeable with Yamnaya Samara in my models.

So unless you can put forward a convincing argument that a population basically like Yamnaya came into existence in the East Baltic from a mixture of Latvia MN2 outliers, thus far unknown anywhere near the Baltic Caucasus Hunter-Gatherers, and indeed also Lengyel-like farmers, then we're simply stuck with a migration from the steppe to the East Baltic.

But Yamnaya Samara can be modeled as Latvia MN, with and without Karelia HG in the outgroups. In fact, the statistical fit is better than with Karelia HG as part of the Eastern HG reference pop.

This is probably because Latvia MN2 is closer to the Eastern HG that makes up Yamnaya Samara, perhaps because it's slightly more western than Karelia HG.

What this might mean is that the same North Eurasian R1b foragers that pushed occasionally as far west as the Baltic also populated the Caspian steppe. Or there may even have been a Mesolithic or Neolithic expansion from near Latvia to the steppe that eventually contributed to the ethnogenesis of Yamnaya.

Very interesting if true, but, nevertheless, totally irrelevant to the obvious conclusion that there was a migration, or migrations, of Corded Ware people like Latvia LN1 from the steppe to the Baltic during the LNBA.

Unless of course you can come up with a convincing counter hypothesis? And I don't mean that you just blather on about Latvia LN1 being ~50% Latvia MN2, with the rest totally unaccounted for, I mean actually try and come up with something intelligent and plausible.

Davidski said...

Unless you and Davidski want people to keep proposing "an expansion of basically unadmixed Caucasus Hunter-Gatherers across the northern half of Europe" which they have every right to with the current analysis. How does one strip that right and reinforce the ideas that Davidski has proposed?

You can propose anything you want, as long as it's plausible and worth reading. Thus far, neither you nor anyone else here has come up with a valid proposal how a mixture of Latvia MN2 with CHG could have taken place anywhere near the Baltic.

Show that the EHG transmitted via steppe expansions comes predominantly from one place neighboring the CHG homelands that could support a steady CHG introgression over time rather than a major independent CHG migration.

Why do I need to show this?

Why does the CHG admixture need to be steady? Why not sudden, caused by the sudden increase in mobility and wealth on the steppe? Wouldn't this fit the Caucasus brides theory?

mickeydodds1 said...

Cockfight central, Australia.

Rob said...
This comment has been removed by the author.
Ric Hern said...

Globular Amphora predates Corded Ware in that area. Globular Amphora bordered the Narva Culture.Could something ancestral to Globular Amphora be the source of those R1b individuals ?

Seinundzeit said...

Rob,

When couched in that language, it doesn't seem like you disagree with David, in any "deep" sense.

I don't think David is suggesting that this Latvian sample came straight from the "Samara Bend" or something.

Like you, he seems to be arguing that this Corded Ware sample is the product of those same processes of populational fusion and dynamism which led to Yamnaya. That's quite a different proposition, one which doesn't entail any simple cookie-cutter scenario.

It seems that where you truly disagree with him is in your understanding of the role played by CHG-related peoples.

If I'm not mistaken, perhaps you think that CHG is essential for understanding the PIE question, in terms of temporal priority, in terms of the very roots of that language family, and in terms of comprehending the mechanisms of expansion for all of these populations?

Seinundzeit said...

human443,

Hmm, I'm going to go out on a limb here, and assume that you completely missed everything I wrote right in between those paragraphs:

"But, the population genetic picture remains rather unchanged, with regard to affinities and proportions.

I mean, both Yamnaya and this Latvian Corded Ware samples are the product of mixture/hybridization between EHG-related and CHG-related ancestries, with some minor Neolithic European-related admixture. Note the use of the word "related". Very important.

And, considering the interchangeability between Yamnaya and this Latvian Corded Ware sample, it's clear that Latvia_LN1 was of steppe origin.

Nothing seems to have changed."

I try my best to be unambiguous.

Again, genetically speaking, Yamnaya and this Latvian Corded Ware sample are virtually identical.

So, it doesn't take some radical act of loose/wild deduction, to figure out that both Yamnaya and this Latvian Corded Ware individual represent the same processes of populational fusion and dynamism.

Basically, we're dealing with the same stream of ancestral populations in both cases, and it seems that even the proportions are the same.

Like David, I really fail to see the parsimony of assuming a migration of CHG-related peoples into Northeastern Europe, who then meld with ancient EHG-related people already living there, and thus by means of pure accidental contingency this mixture between incoming Caucausians and local hunter-gatherers leads to a population that is virtually identical to Yamnaya.

"Occam's Razor" is actually an important scientific principle, one which is meant to be followed. Yet, very few people in these amateur online discussions seem to give much thought to it.

Anyway, with regard to my use of the term "heated", that really was a euphemism on my part.

If you've been following the comments section, I would hope that you've noticed the presence of some really "crazy shit".

Essentially, I'm just puzzled as to why this paper seems to have attracted some "kooky" commentary/discussion.

Other than the weird discussions, like the one a few days ago about height differentiation in prehistoric populations (like, WTF were they talking about? Was that particular commentator high/drunk/both?), I have no problem with vigorous debate.

So again, "heated" was in reference to the weird stuff, like "Neolithic Europeans were a superior race destined to conquer the world", or “no, Bronze Age Steppe populations were obviously way cooler”, and all the other strange/odd material that was posted.

And again, intense/heated scholarly discussion is good, and very much essential. Please, note the word "scholarly".

Arza said...

@human443
You need to throw an EHG into the outgroups

It was just an experiment - what happens if one will throw out "Samara" from Yamna Samara.

the most logical being the one that has the least likelihood of having any DIRECT mixture into modern populations

If I was reading correctly some comments made here about Srubnaya Outlier then probably there were some ANE-rich people still lurking in the neighbourhood.

Yamnaya_Samara should prefer Samara_HG or Samara_Eneolithic.

Population,Kotias:KK1,Latvia_MN2:ZVEJ31,Samara_Eneolithic:I0433,Samara_Eneolithic:I0122,D statistic
Yamnaya_Samara:I0231,38,42,4,16,0.0058
Yamnaya_Samara:I0357,42,54,0,4,0.0127
Yamnaya_Samara:I0370,39,32,27,2,0.0056
Yamnaya_Samara:I0429,40,60,0,0,0.0056
Yamnaya_Samara:I0438,34,30,10,26,0.0039
Yamnaya_Samara:I0439,39,39,0,22,0.005
Yamnaya_Samara:I0441,42,53,0,5,0.0081
Yamnaya_Samara:I0443,44,42,11,3,0.0055
Yamnaya_Samara:I0444,40,60,0,0,0.008

Population,Kotias:KK1,Latvia_MN2:ZVEJ31,Samara_Eneolithic:I0434,Samara_HG:I0124,D statistic
Yamnaya_Samara:I0231,40,32,0,28,0.005
Yamnaya_Samara:I0357,37,48,15,0,0.0124
Yamnaya_Samara:I0370,41,29,0,30,0.0052
Yamnaya_Samara:I0429,40,60,0,0,0.0056
Yamnaya_Samara:I0438,39,28,0,33,0.0038
Yamnaya_Samara:I0439,43,40,0,17,0.0053
Yamnaya_Samara:I0441,43,55,0,2,0.0081
Yamnaya_Samara:I0443,45,40,0,15,0.0054
Yamnaya_Samara:I0444,39,52,0,9,0.0078


It looks like Latvia_MN2 is indeed preferred, at least by 4mix using Global 10.

I think that the switch from Karelia_HG to Latvia_MN2(-like) helps to clear one thing - for me it was weird that Yamna required some farmer input, but suddenly farmer-less Latvia_LN1 popped out between Yamna and the farmers. MN2 solves this puzzle - no farmer, no cry.

human443 said...

@ Davidski

"Really not sure why you're saying that, since, like I said, Latvia LN1 is very much interchangeable with Yamnaya Samara in my models. So unless you can put forward a convincing argument...etc."

You are the one saying you have proven it, thus you need to do the due diligence to make sure you have covered every angle. I need not put forth an argument about anything.

"But Yamnaya Samara can be modeled as Latvia MN, with and without Karelia HG in the outgroups. In fact, the statistical fit is better than with Karelia HG as part of the Eastern HG reference pop."

Excellent, let's see the numbers and keep them coming.

"You can propose anything you want, as long as it's plausible and worth reading. Thus far, neither you nor anyone else here has come up with a valid proposal how a mixture of Latvia MN2 with CHG could have taken place anywhere near the Baltic."

Anyone can propose anything that is possible, if you wish to say you have proven a possibility false, you need to demonstrate the data that does so.

"Why does the CHG admixture need to be steady? Why not sudden, caused by the sudden increase in mobility and wealth on the steppe? Wouldn't this fit the Caucasus brides theory?"

Steady and sudden are relative terms and should be elaborated further...5% CHG in Samara_HG, 25% in Samara_Eneolithic, 40% in Yamnaya_Samara...that is steady (A continual increase over an extended time). That fits the Caucasus brides theory. A sudden increase would not be suggestive of an introgression, but rather a migration.

"Why do I need to show this?"

To show that the source of the massive bronze age migration is indeed a ~50/40/10 mixture of EHG/CHG/EEF out of the (what did you propose?) Dnieper Don region? Instead of something heavier in CHG that picked up some of the EHG that surrounds it in nearly every direction.

Ric Hern said...

How related were the Samara Culture to the Dnieper-Donets Culture ? Some point to a possible genetic relation between the two. If so then it is not surprising to see a broadly similar people living between Poland and the Southern Urals at +-7000 years ago. Or am I way wrong ?

Davidski said...

@human443

You are the one saying you have proven it, thus you need to do the due diligence to make sure you have covered every angle. I need not put forth an argument about anything.

To every reasonable person reading what I said here I have proven it beyond a reasonable doubt.

Considering the data I posted, there's simply no reasonable way to interpret the presence of Latvia LN1 in the East Baltic at that time than to say she was of migrant stock from the steppes.

You can keep doubting this, asking for more evidence, and refusing to logically counter my arguments, but you just look mentally unstable when you do.

@Al Bundy

No idea what Bradley said. The tickets were $600, so the people I knew in San Diego said no way.

It makes no difference though. If we keep getting these sorts of results, with R1a and R1b all over Mesolithic and Neolithic Eastern Europe, and these Yamnaya clones popping up all over Europe during the LNBA, then it's game over.

Next big paper I reckon it's game over, with R1a-M417 and R1b-M269 expanding out of the Pontic Steppes in all directions.

Davidski said...

@Al Bundy

Yeah, I know the argument. It strikes me as an emotional one, simply driven by the need to put the origins of PIE outside of Europe in a more exotic location than the Eastern European steppe.

The CHG or teal component is used to justify it, but there's been no real effort to explain how and why it got to Europe. The argument thus far is simply that it's there, and so it might represent PIE speakers from the exotic south.

But most people who understand this debate will know it's game over when R1a-M417 and R1b-M269 show up in early Kurgans on the steppe, probably north of the Black Sea, rather than in any ancient farmer or herder remains from the Near East. And on top of that, it also becomes clear that the CHG or teal on the steppe came with women.

The debate might continue after that in academia, with papers arguing for the South Caucasus or whatever as the PIE homeland, but like I say, it'll be all wrapped up at that stage, and I think most of us will be discussing other things.

Arza said...

A map:
https://4.bp.blogspot.com/-B0gkE1-gBNI/WJmfHax-kHI/AAAAAAAAAGk/d0vnNG6AbAMQ9c-XtMJdPpmDmueZ-kx8wCLcB/s1600/kotias.jpg

Radius of circle - 900 km. Almost perfect correlation of geography and PCA. And as on PCA - Latvian_LN1 is closest to the CWC area.

Ariel said...

About the game changers... Some nmonte results like this one make sense to me. Invasion(Yamna/steppe)+drag(people in the between from eastern Europe)+natives(farmers/HGs)

Swedish
"LBK_EN:I0054" 44.8
"Latvia_MN2:ZVEJ31" 27.25
"Yamnaya_Samara:I0441" 18.3
"Latvia_MN1:ZVEJ26" 9.6
"BedouinB" 0.05

Davidski said...

Now Haak and the Max Planck team have a hybrid theory you've also written about. Pure conjecture because as you say they don't seem to have much else?

That Max Planck teams includes ardent supporters of the farmer PIE hypothesis, one of whom has basically trashed the Kurgan hypothesis in the past. So make of that what you will.

It makes no difference what they come up with. The only thing that counts is the data they put out, and they have funding to sequence a lot of ancient DNA.

Davidski said...

@Ariel

Getting creative with nMonte won't help you.

Rob said...

@ Sein

I agree with your summation. Believe it or not, as basic & reasonable as your statement was, some people can't grasp my statements, and start talking about the Irish Mesolithic foragers.
Anyhow, let's have a little look at some runs using some very fundamental groups (more detailed on the hunter-gatherers, lighter on EEF distinctions):


Afanasievo:RISE508
Kotias:KK1 43.4 %
Samara_HG:I0124 36.25 %
Latvia_HG:ZVEJ32 20.3 %
Ukraine_HG1:StPet2 0.05 %

Yamnaya_Samara:I0429
Samara_HG:I0124 43.15 %
Kotias:KK1 36.5 %
Latvia_HG:ZVEJ32 11.15 %
Ukraine_HG1:StPet2 9.15 %
Latvia_HG:ZVEJ25 0.05 %

Maros:RISE373
Hungary_N: 31.05 %
Kotias:KK1 18.7 %
Barcin_Neolithic:I1099 12.9 %
Hungary_HG:I1507 19.65 %
Latvia_HG:ZVEJ32 5.75 %

Hungary_BA:I1502 (Mako culture)
Hungary_N:I1495 44.8 %
Motala_HG:I0012 17.65 %
Latvia_HG:ZVEJ32 16 %
Kotias:KK1 12.15 %
Loschbour:Loschbour 9.2 %


Corded_Ware_Germany:I1534
Kotias:KK1 32.25 %
Latvia_HG:ZVEJ32 29.95 %
Samara_HG:I0124 24.25 %
Hungary_N:I1495 13.55 %

BattleAxe_Sweden:RISE94
Kotias:KK1 30.25 %
Ukraine_HG1:StPet2 27.95 %
Hungary_N:I1496 17.7 %
Motala_HG:I0012 10.1 %
Villabruna:I9030 7.75 %


Bell_Beaker_Czech:RISE568
Latvia_HG:ZVEJ32 52.45 %
Hungary_N:I1495 29.15 %
Kotias:KK1 18.35 %
Barcin_Neolithic:I1099 0.05 %


BB Germany gets interesting:

Bell_Beaker_Germany:I0111
Iberia_EN:I0410 33.45 %
Latvia_HG:ZVEJ32 31.75 %
Kotias:KK1 26.4 %
Karelia_HG:I0061 8.35 %


There is the Late Neolithic- EBA transition in a nutshell.
I've stated multiple times Ill refrain from making any sweeping deductions about linguistics before I see data from Rakhi and Mycenean Greece, otherwise now matter how solid we believe our deductions are, the reality is we have no evidence what language CWC or BB spoke. So we need an actual 'anchor' with attested language.
But really, it's not rocket science- with all the information today available on the internet, its easy to deduce what was happening in 3800 BC, and where was the centre of spread of new metal technologies and chiefly societies, so it's rather bewildering how so many people are so ignorant still, in denial, or whatever.

The only unifying component is Kotias: and the only place I can think where a predominanlty CHG-like population to have existed is the north Caucasus, perhaps since the Mesolithic, but of course we need actual data, because I have no doubt the aforementioend region has seen a multitude of changes in itself.

BTW: this was was run using weighted data as you had used, compiled kindly by Alberto

Tomorrow we can look at South Asia & some Uralics

Ariel said...

IMO there are still 3 unsolved mysteries about Europe recent genetic hystory.
1) The resurgence of WHG admixture in northern Europe.
2) Different EHG to CHG ratio in northern Europe compared to Yamna.
3) Extra CHG in southern europe that doesn't really correspond to the admixture ratio of any modern middle eastern populations. (Maybe except Cyprus)

My solutions are.
1) Drag from eastern Europe/baltic area (the only places with late WHG)
2) Drag from eastern Europe or western steppe/Ukraine (alternatively a early steppe herders expansions [Anthony])
3) Two very late expansions from Anatolia or the levant (one that brought Greek from Armenia and one that was Etruscan-like)

jv said...

I find this very interesting because the more I know about the ancient migrations of R1b & R1a, the more I may know about when my ancient Grandmothers entered the Pontic-Caspian Steppe. Steppe lineages like mtDNA H13 origins are from the Caucasus or so I believe that's current train of thought. So I wonder if my mtDNA H6a was in the Caucasus during the LGM then expanded to the Steppe when conditions improved or did mtDNA H6a spend the LGM in the Central Russian Plains or in the Ukraine. H6a is approx. 9503.8 years old and mother clan H6 is approx.10,945.6. I've read articles that say mtDNA H6 originated in Central Asia because H6 has a strong presence there today. H6 was found in the Andronovo Culture(H6a1b Okunev Culture) so she migrated from the west(Ukraine & Russia) to the east thousands of years ago. I think this current population increase of H6 in Central Asia is due to natural selection or something else. I find it rather misleading coming across information that says: FROM CENTRAL ASIA INTO EUROPE-(H6, H6a, H6a1a, H6a1b are included as well as many H13's, H2's, U2's, W1's, W3's, ) Didn't some of these lineages originate in Eastern Europe AND then expanded East. I like this research and plan to stay with it. I'm waiting for more finds. Maybe someday I'll get the answers I want. In the meantime, I better get to reading all of the 2015 post on this Blog. Seems 2015 was the Year of the Yamnanian! jv

Jaydeep said...

Dear Rob,
I agree with your general thrust. It is baffling why people should try to deny the role of CHG in the PIE equation. European archaeologists as well as Anthony have argued for Yamnaya as the place of PIE. Yamnaya was clearly different from the preceding steppe cultures. And aDNA has shown that one of the distinguishing features of Yamnaya which make it stand out from preceding steppe cultures is the high CHG.

So it is natural to think that the people who are responsible for the CHG input in Yamnaya might also have a very fundamental role in the formation of the Yamnaya culture including its linguistic base. In other words IE languages might themselves have come to the steppe with the CHG people.

Ofcourse, I do not think that CHG of the Caucasus was indeed the real source of this southern input into the steppe. It could have come from anywhere between Iran and South Central Asia. Considering that Iran, Central Asia and South Asia have had some of the earliest Neolithic societies and had very advanced societies during Bronze Age and also have been known to speak IE languages from a very early period, this looks like a reasonable suggestion.

Take the case of the Indus civilization. Inspite of attempting to prove since many decades that this civilization spoke some sort of Dravidian, scholars have singularly failed to do so. Why could this civilization not be Indo-European ? There is no credible explanation to such a question.

Kristiina said...

@Gravetto Danubian, I understand your interest in Majkop from the linguistic point of view. A very influential language family, such as the IE language family, should be derived from an important centre of cultural and economic progress and not from any remote sparsely populated area.

It is interesting to note that the biggest grammatical difference between IE languages and Uralic/Turkic languages is the absence of gender in the latter group, while the gender systems are typical for West Asian languages such as Semitic/Afro-Asiatic and Northeast Caucasian languages; and for Dravidian languages (http://wals.info/feature/31A#2/25.5/148.4; http://wals.info/feature/32A#4/21.04/62.40; http://wals.info/feature/30A#2/25.5/148.4).

I agree that the West Asian / CHG element of IE migrations should not be downplayed and reduced to only some female input.

I find very interesting that pre-R1b-M73 was found in Mesolithic Latvia, because it could be an indication of Mesolithic migration from Latvia/Lithuania/Belarus to Samara area. Are you aware of any such archaeological movement from west to east c. 10 000 – 6000 BC?

mickeydodds1 said...

Jaydeep,
Bones cannot speak.

Jaydeep said...

Thats true but what is your point ?

Nirjhar007 said...

Yes Rob, will love to see how S Asians will perform tomorrow :) .

Karl_K said...

@human443

"How does one strip that right and reinforce the ideas that Davidski has proposed? Show that the EHG transmitted via steppe expansions comes predominantly from one place neighboring the CHG homelands that could support a steady CHG introgression over time rather than a major independent CHG migration."

This will eventually be shown using extremely high quality phased ancient genomes. The only way to get those is from close family groups. For some populations, thise will be hard to obtain. For others, they will be easier.

With high quality phased genomes, you can show how long the stretches of various ancestry are, and look at very rare alleles.

With that kind of data, nobody will suggest unadmixed anything persisting past a certain date.

AWood said...

@Jaydeep,

If linguistic contact puts PIE speakers between Uralic and Caucasian language families, and let's say some vocabulary indicates a steppe habitat, I anticipate a Russian origin of this language family. We can't make special pleading cases simply because the level of CHG rises over time.

EastPole said...

Interesting article

https://archaeologynewsnetwork.blogspot.com/2017/02/baltic-hunter-gatherers-adopted-farming.html#o4SQWGGO1JDraCk3.97

Grey said...

Rob

"The only unifying component is Kotias: and the only place I can think where a predominanlty CHG-like population to have existed is the north Caucasus, perhaps since the Mesolithic"

your model makes sense on the surface (and is what i originally thought most likely) but currently the ydna vs mtdna seems to contradict it

#

Jaydeep

"It is baffling why people should try to deny the role of CHG in the PIE equation."

currently, ydna vs mtdna seems to contradict it

#

Kristiina

"I agree that the West Asian / CHG element of IE migrations should not be downplayed and reduced to only some female input."

It's not being reduced to; it's what the data currently implies.

The problem is the other way round - people not wanting to believe a bunch of barbarians could have been the spark of it.

#

"A very influential language family, such as the IE language family, should be derived from an important centre of cultural and economic progress and not from any remote sparsely populated area."

I tend to agree with this bit which makes me wonder if there are some very rich tombs of kargaly copper kings (from before their displacement) buried in that region somewhere.

Grey said...

Ariel

"3) Extra CHG in southern europe that doesn't really correspond to the admixture ratio of any modern middle eastern populations. (Maybe except Cyprus)"

If PIE/IE's first big conquest expansion (as opposed to other kinds of expansion) was of that part of the steppe colonized by farmers (in the process picking up a big chunk of chg mtdna) then i'd suggest a likely side-effect of that would have been a flood of displaced chg ancestry south into the Balkans, Anatolia and Mid-East.

Ryan said...

@Kristiina - "A very influential language family, such as the IE language family, should be derived from an important centre of cultural and economic progress and not from any remote sparsely populated area."

History and pre-history are filled with examples of successful cultures emerging from the interface zones between older cultures. Hence Ibn Khaldun's work. I think it's exceedingly plausible that an influential language family would emerge from the boundary between hunter-gatherer and agriculturalist ways of life.

Rob said...

@ Kristiina

Yes the CHG exogamy arguments fails, because if that were the case, it should be a homogeneous Samara/CHG or Ukraine /CHG admixing block far and wide, but that's clearly not the case, despite attempts to "wiggle" the data .





As for R1b, I can't think of any Baltic -> Samara movement, but can think of a Urals/Samara movement to Baltic with pressure blades or eastern neolithic pottery. However the date of that is too late to explain the Villabruna. The loan "stray wander" scenario is unconvincing. The only reasonable link between Italy, the Baltic and Urals (based on archaeological evidence) is a movement from a fourth source during post Ice Age period- which would be the EpiGravettian which connected Italy the Balkans and Eastern Europe

Rob said...

@ Grey

Given that your comments are always founded
on deep empirical evidence, please elaborate on "but currently the ydna vs mtdna seems to contradict "?

Samuel Andrews said...

Btw,

Ancient mtDNA update.

Catacomb
I just realized some of the "Catacomb" mtDNA is from Germany and Poland. The samples belong to typical EEF haplogroups; including H1, J1c, and K1a. They also had a high frequency of blue eye alleles. Most of the EEF-like mtDNA in my Steppe data base came from those samples. When they're removed a more clear picture of Catacomb mtDNA is drawn.

Catacomb mtDNA is relevant to the Ukraine HG/N genomes and the debate of whether they contributed to modern Europeans. Catacomb had 30% U4, while Yamnaya had 4%. Catacomb had as much U5a as Yamnaya, about 20%. Catacomb's mtDNA is barely Middle Eastern, they almost look like European hunter gatherers. They *may have!* not packed the CHG needed to be the source of Steppe ancestry in modern Europeans.

Rob said...

@ AWood

Did you know there is no such thing as Caucasian language family, in other words there are actually three 3 distinct "Caucasian language" families ? So which are you referring to ? They'd all have different relationships to PIE
Have you also considered that the "Caucasian languages" , at least some of them, might be themeselves intrusive to the Caucasus
So would you care to elaborate which morpho-syntactic features support your conclusions ?

Tesmos said...

@Samuel Andrews

What do you think about mtdna haplogroup HV1 in MBA Babino?

http://www.anthrogenica.com/attachment.php?attachmentid=13775&d=1486089230

human443 said...

@ Davidski

I'm not going to address your last response, it is clear that English is not your first language, and that most of this is a misunderstanding.

To prove your case. Simply do the following.
1) Do some nmonte runs on Yamnaya, Latvia_LN1, Bell Beaker, and something on the eastern frontier of things (Andronovo/Sintashta?) using as sources all of the new mesolithic + neolithic samples, Samara_HG, Samara_Eneolithic, Motala_HG, the various WHG, various middle and late neolithic European farmers, and the middle eastern chalcolithic populations using column/outgroup populations that consist of at least...
AG3-MA1
Barcin_Neolithic
ElMiron
Iran_Neolithic
Karelia_HG
Karitiana
Kostenki14
Levant_Neolithic
Papuan
Ust_Ishim
Villabruna

2) More outgroups may be added depending on the results (i.e. if Latvian_HG does not show as a contributing population to any of the test subjects, add it to the outgroups).

3) Once all outgroups possible have been added and the nmonte models from that test is completed. Run those models through qpadm to confirm.

Davidski said...

@human443

I'm not going to address your last response, it is clear that English is not your first language, and that most of this is a misunderstanding.

Thanks for the comic relief. But my earlier reply to you stands...

To every reasonable person reading what I said here I have proven it beyond a reasonable doubt.

Considering the data I posted, there's simply no reasonable way to interpret the presence of Latvia LN1 in the East Baltic at that time than to say she was of migrant stock from the steppes.

You can keep doubting this, asking for more evidence, and refusing to logically counter my arguments, but you just look mentally unstable when you do.

Olympus Mons said...

Has it been proven already that “my” Shulaveri-Shomu of the land of the original CHG , 6th millennium BC, is the source of PIE and R1b-M269? – Not yet? Ok bye.

Davidski said...

Has it been proven already that “my” Shulaveri-Shomu of the land of the original CHG , 6th millennium BC, is the source of PIE and R1b-M269? – Not yet? Ok bye.

What does CHG got to do with R1b? Nothing.

Olympus Mons said...

Davidski, Davidski...

here we go again. Really simple. Shulaveri had a high R1b paternality gotten probably from something in western black sea, mixing with Barcin in south Black sea and later getting lots of CHG admix when as Fikertepe were moving eastern bound via south shores of Black sea (mixing there with more pure CHG in 7th M), towards the south Caucasus where they became Shulaveri-Shomu. there M269 appeared.

Shulaveri gave r1b-L23 and PIE to steppe after disbanding on 5th millennium.

well, my old, weird story that I rant for so long. right? what are now those Max planck dudes doing by agreeing with me?

Grey said...

Rob

"Given that your comments are always founded on deep empirical evidence, please elaborate on "but currently the ydna vs mtdna seems to contradict?"

Are you saying the ydna vs mtdna argument is not now the key issue?

My comments are based on skim reading the evidence and throwing in hopefully relevant additions from other areas like: wheat doesn't like acid soils, the historically attested Numidian light cavalry from the classical era didn't use saddles, stirrups or bridles, or that before humans were slowly pacified by farming they were mostly wolves.

http://ukcommentators.blogspot.co.uk/2006/11/sudan-incident-1909.html

Also reading people. I'm good at that.

#

"Yes the CHG exogamy arguments fails, because if that were the case, it should be a homogeneous Samara/CHG or Ukraine /CHG admixing block far and wide, but that's clearly not the case, despite attempts to "wiggle" the data."

steppe groups and chg bordered each other for a long time so any chg mixture could have changed over time

a said...

Olympus Mons said...

Shulaveri gave r1b-L23 and PIE to steppe after disbanding on 5th millennium.

well, my old, weird story that I rant for so long. right? what are now those Max planck dudes doing by agreeing with me?


Diversity of ideas is a good thing.

There are sooo many qualified posters, including Eurogenes, that could take the raw tested data[ our shared European ancestors] and run programs to parse the ancestral components[brick and mortar buildings are obsolete-in relation to flow of data]. I would venture a guess, within 24 hrs you would have your answers if the raw data was made public[100-200 samples]. It would be so much easier to release the results 5-10 at a time on a daily basis. You could see real time pca plots on a daily basis[new samples added weekly or daily. All this could be done on a volunteer basis.
----------------------------------------------------
https://en.wikipedia.org/wiki/Max_Planck_Society

The society has a total staff of approximately 17,000 permanent employees, including 5,470 scientists, plus around 4,600 non-tenured scientists and guests.[2] Society budget for 2015 was about €1.7 billion.[2]

truth said...

HOw can R1b be of CHG origin, when the mesolithic R1b samples have 0% of CHG ?

Davidski said...

@Olympus Mons

What does R1b have to do with Barcin farmers? Nothing.

Ric Hern said...

Hittite = Ezero Culture ?

Antoni Małkowski said...

„Romulus said...
@Antoni

You made such a nice map too bad it's completely wrong. Awwww.”

Somebody was smoking marijuana. I do not.

epoch2013 said...

@Olympus Mons

"The is no BB dna. So does not require anything.
Germany sample were half breeds between CWC and BB."

This implies that you know what BB is. However..

"When we have REAL Bell beakers then we will see."

..you seem not to have samples. That is extremely odd. What is it that you have that makes it so clear that the ONLY samples we have from BB sites are not truly BB?

epoch2013 said...

@Antoni Małkowski

Wasn't me. I quite two decades ago.

epoch2013 said...

@Rob

The poor fit of pure CHG + EHG for Yamna ancestry is not necessarily proof for the fit in Lazardis 2016 paper. IIRC CGH + EHG is a better fit than Iranian Early Neolithic + EHG for Yamna (Can someone back this up?). That means, in my very humble opinion, that if you are to defend the position that a lot of Yamna ancestry originated in Iran it actually would have to have come to Iran *after* the early neolithic.

So where did it come from?

Lazardis showed that Iran Chl is more of a mixture between Anatolian and Iranian/CHG than earlier Iranians (see PCA). That certainly opens the possibility that the Iranian Chl fit actually masks a partial EEF admixture. Dave did some tests here. CT would be a big possibility here.

Rob said...

@ Epoch
I think you've confused me with someone ?
I don't recall saying anything about Iran Neolithic or Chalcolithic

Moreover I don't think it's a case of any "confusion". It's not possible to link Chalcolithic to a confounding effect of Balkan or CT farmers ; the two are completely different; and Iran Chalcolithic is irrelevant for Yamnaya.
But let's now note that Ukraine Neolithic had barely any CHG, which makes the likelihood of CT being the source of "CHG" in Yamnaya and Europe as a whole rather unlikely barring some odd "leap-frog" phenomenon

Rob said...

Big Al
I agree with the General chronology and scheme you outlined, and that the steppe was a very important vector relaying impulses to Europe, but neither the originator of these changes, nor the demographic bed.
That centre was the Majkop culture, but note it was but one centre (the were others and other components of a "package").
At this stage i don't think we can really tell where the major lineages of R1a and R1b came from - could be anywhere between the Baltic and Kuban; if more northern then it means we are dealing with "kurganized" Baltic-Eastern European locals.

Rob said...

Yes he does all the hard work.
I'm just a monkey pressing buttons

Matt said...

Davidski responding to Sam wrote: Hungary_BA
Caucasus_HG 0
Latvia_HG 0.317
Latvia_LN 0.049
Lengyel_LN 0.634
chisq 12.843 tail_prob 0.303704


Just noticed this upthread and it was a cool idea to test. How do these models for HungaryHG compare to if you used La Brana/Loschbour/Bichon/KO1?

Does Hungary_BA then need Samara / Karelia HG, or is it still perfectly able to be modelled. I'm thinking LatviaHG here approximates a population clinal on KO1->UkraineHG.

Hungarian Bronze Age BR2 is known from Cassidy's median haplotype analysis to have contributed more to modern East European populations (Poland peak) - http://s22.postimg.org/5y9hc69ip/br2.jpg?noredir=1. (Same analysis where there are evident differences in descent from Western European MN Ballynahatty, Loschbour and early Irish Bronze Age in the west). This qpAdm models it as almost Barcin+Latvian HG, and no CHG (in agreement with unsupervised ADMIXTURE), with more HG balance than typically present in Iberian populations (except the one Iberian Bronze Age sample - ATP9 - from mid LNBA period which looks almost half HG with again no CHG - further samples needed for that population!).

So I suppose if we think of BR2 (y-dna haplogroup J2) as a population which combined lots of Barcin Neolithic with Ukraine and Hungarian HG ancestry, might make a good "other side" to a Corded Ware / Yamnaya influx for Eastern Europe? Less so for West Europe where the Iberia Chal pop might be more useful.

None of this is probably novel thinking to a lot of you lot - I was previously thinking of BR2 as a population which *had* to be Yamnaya influenced, but in this context of now having firmed up that we already have HG intermediate between WHG and EHG in the area, pre-Yamnaya, it may not be, and instead it's more like the Chal pops in Western Europe (just Barcin enriched with HG and with none of the CHG that is a "tell" of the Yamnaya's influence).

(High coverage and haplotypes will elucidate so many of the fine details.)

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

@Matt

So I suppose if we think of BR2 (y-dna haplogroup J2) as a population which combined lots of Barcin Neolithic with Ukraine and Hungarian HG ancestry, might make a good "other side" to a Corded Ware / Yamnaya influx for Eastern Europe?

Nah, doesn't seem very likely considering that BR2 is a Late Bronze Age individual and does show quite a bit of Yamnaya-related ancestry in most models. The model above was actually for both BR1 and BR2.

Matt said...

Davidski: Nah, doesn't seem very likely considering that BR2 is a Late Bronze Age individual and does show quite a bit of Yamnaya-related ancestry in most models. The model above was actually for both BR1 and BR2.

BR1 maybe a better "other side" for East Europe, though that would lack the direct haplotype evidence (and is more assuming BR2 has continuity with BR1). Can you test BR1 and BR2 individually?

Davidski said...

Matt, I can't see any indications that these two might represent relict Eastern European samples from the Chalcolithic, since both have late dates in the scheme of things and are obviously very mixed. If you're looking for a Chalcolithic reference for East Central Europe then Hungary CA is probably the best choice, because it's actually dated to the Chalcolithic/Copper Age Late Baden Culture.

Hard to say what these models mean. But probably that the Yamnaya input that shows up for them in many other models came from western Yamnaya, where the forager input was closer to Latvia_HG/SHG than to EHG along the WHG>EHG cline than for Samara Yamnaya.

BR1
Caucasus_HG 0.109
Latvia_HG 0.379
Lengyel_LN 0.512
Yamnaya_Samara 0.000
chisq 9.051 tail_prob 0.617212

BR1
Caucasus_HG 0.000
Latvia_HG 0.402
Lengyel_LN 0.561
Yamnaya_Samara 0.037
chisq 10.789 tail_prob 0.461079

BR2
Caucasus_HG 0.120
Latvia_HG 0.193
Lengyel_LN 0.687
Yamnaya_Samara 0.000
chisq 12.005 tail_prob 0.363277

BR2
Caucasus_HG 0.000
Latvia_HG 0.207
Lengyel_LN 0.738
Yamnaya_Samara 0.055
chisq 13.713 tail_prob 0.249292

Alberto said...

I think that the haplotype analysis in Cassidy et al. does suggest that BR2 has CHG admixture (actually in a higher CHG/EHG than Rathlin). Which makes it plausible that if it has Yamnaya admixture it is from Western Yamnaya (if it gets confirmed that western Yamnaya was SHG/CHG).

And it's nice to see that with the individual analysis, qpAdm mostly agrees with Global 10:

Hungary_BA:I1504
Hungary_N:I1495 46 %
Latvia_HG:ZVEJ32 33.3 %
Kotias:KK1 18.5 %
Loschbour:Loschbour 2.2 %
Barcin_Neolithic:I0707 0 %
Yamnaya_Samara:I0231 0 %
Hungary_HG:I1507 0 %
Karelia_HG:I0061 0 %

Distance 0.001544

And this explains all all the models with modern Europeans, where Admixture, PCA data and direct D-stats detect a shift from EHG to WHG compared to what would be expected from a 40-50% Yamnaya_Samara admixture in northern Europe. Given that Ukraine_HG is about 50% WHG and 50% EHG, then it all makes sense statistically (and probably in other ways: geographically, demographically, archaelogically,...)

Matt said...

Runs are without Yamnaya in pleft vs without CHG? Odd that the two Hungary_BA have substantially more CHG in that run than Yamnaya_Samara in that run (I would have expected that as CHG is only 35-45% Yamnaya that you would need around 2x Yamnaya as CHG or 20%).

Alberto: I think that the haplotype analysis in Cassidy et al. does suggest that BR2 has CHG admixture (actually in a higher CHG/EHG than Rathlin).
How so? Like in terms of this relationship, how so, http://i.imgur.com/y7fQu8Y.png

Alberto said...

@Matt

Yes, in the sense that if BR2 was a straight mix of Europe_MN + EHG (like Admixture was showing), you wouldn't expect that populations that are low in WHG and very low EHG, but presumably high in CHG (Cypriot, Turkish, West Sicilian,...) would be as high in the list as North Europeans (who clearly have more of both WHG and EHG).

Ir Pegasus said...

"Given that Ukraine_HG is about 50% WHG and 50% EHG"


It's error. Ukraine_HG is EHG, to which the addition of ~25% WHG. He was light-skinned and brown-eyed, in contrast to the dark-skinned and light-eyed WHG. It is not the SHG, it was 3000 years earlier than Motala.

Matt said...

Hmm.... I don't find that so persuasive - Sardinians are slightly above the line, CHG heavy populations like Lezgin, Georgian, Adygei are neutral, likely EHG heavier populations are above the line or neutral. I would ascribe any tendency for East Mediterranean populations to share more haplotypes with to BR2 not to relationship to CHG, but to the greater specificity of its Barcin_N type ancestry to Southeastern Europe. Haplotype donation will be more specific like that. A CHG related pattern would be most obvious in Caucasus+Iranian populations, not Southeastern European populations plus Anatolia.

Alberto said...

@Matt

This is something rather difficult to prove, obviously. If you find strong reasons to think that the AN component is BR2 is very akin to the one in West Sicilians, Cypriots or Syrians, but markedly different from those in Belarusians and Poles, and at the same time don't find strong reasons to think that the WHG/EHG in BR2 is close to that in Belarusians and Poles, then yes, that could explain the results too that they all share similar amount of haplotypes with BR2.

I find more compelling the explanation that the model from Global 10 is more correct than the one from Admixture.

@Pegasus

I don't think that skin or eye color matter here at all. What I get for Ukraine_HG is something like this:

Ukraine_HG1:StPet2
Karelia_HG:I0061 45.2 %
Loschbour:Loschbour 41.8 %
Kotias:KK1 13 %

Distance 0.003748

But in any case, Latvian_HG is a better fit than Ukraine_HG, and Latvian_HG is even more western. So that's the relevant point here.

Matt said...

Alberto "AN component is BR2 is very akin to the one in West Sicilians, Cypriots or Syrians, but markedly different from those in Belarusians and Poles, and at the same time don't find strong reasons to think that the WHG/EHG in BR2 is close to that in Belarusians and Poles
Why is that necessary (that either of the AN or HG in BR2 is dissimilar to that in Belarusian/Polish)?

Ir Pegasus said...

@Alberto
"I don't think that skin or eye color matter here at all." - It's main matter.
EHG and WHG have common part, it is not clear what percentage fall in a component.
Kotias:KK1 13% is fiction component, it is part EHG.
D-statistic gives EHG.

Samuel Andrews said...

Keep in mind...

>There's diversity in BA Hungary genomes. Some look like a HungaryCA+Yamnaya mix, some HungaryCA+WHG/UkrainHG+Yamnaya mix.

>Hungary BA Y DNA results so far are; I2a2a, G2a, R1b.

Alberto said...

@Matt

Because how else would you explain West Sicilian sharing more haplotypes with BR2 than Belarusian?

Caucasus populations are around the line, true, but is that line very significant? And shouldn't it mean, anyway, that BR2 has an amount of CHG that is comparable to that in Rathlin? But less EHG? (hence, not increased affinity with high EHG populations).

It's difficult to figure out exactly the components from those haplotype sharing, but if anything, I think they don't suggest that BR2 is Europe_MN + EHG.

Matt said...

@Alberto: It's difficult to figure out exactly the components from those haplotype sharing, but if anything, I think they don't suggest that BR2 is Europe_MN + EHG.

Yeah, I mean I think that's the point I think that the haplotypes don't really tell you very much about the ancient, deep components. They mostly reflect direct recent lineal relationships, whether or not the population which shares the most median haplotype donation is actually the most enriched in the same general components as the ancient it gets the haplotypes from (e.g. is Welsh the most enriched in general European HG just because it gets the most haplotype donation from Loschbour? Probably not.). I'm more convinced by the ADMIXTURE and the qpAdm results more, that BR2 is relatively low in CHG / Yamnaya opposed to Eastern European variants of HG and Anatolian Neolithic ancestry. The thing I really was taking from the haplotype analysis is that BR2 is quite likely to be a real contributor to Eastern European populations / share direct lineal ancestors.

(E.g. compare Ballynahatty vs NE1 and Ballynahatty vs Stuttgart - http://i.imgur.com/Gxm0Yjo.png. Yes, Ballynahatty probably has more Euro HG ancestry than either of those, but the relative sharing doesn't correlate well with that broad Euro HG such that e.g. the most Ballynahatty relative to the others are the most HG. Instead it just reflects fairly areal relationships which represent direct descent (plus a little noise). Doesn't tell you very much either way about relatedness to HG overall.).

Alberto said...

Yes, I agree in that haplotypes would show more direct ancestry, though not decoupled from general ancestry as it's not strictly "recent". And again, for that to work we'd need to explain that direct relationship between BR2 and populations like Sicilians, Cypriots, Armenians and Syrians to the exclusion of Belarusians, Russians or Germans, for example.

But I also agree in that BR2 is high in European HG and not very high in CHG, that's what qpAdm shows and Global 10 mostly agrees (though it's 12% vs. 18% CHG), while quite low in Yamnaya/EHG (only what it would get from high SHG-like admixture).

I checked now Admixture, and I was wrong in remembering that BR2 had no CHG. It's BR1 the one that only gets 1% CHG and 17% EHG. BR2 gets 11% CHG and 17% EHG (and 22% WHG over a baseline of AN). So by Admixture it would be close to Europe_MN + 30% Yamnaya, I guess. (In CHG_K8 that I found from Davidski).

Matt said...

Well, Absolute direct lineal relationship between BR2 and Belorusians, Russians and Germans as measured by median haplotype sharing *is* higher than between BR2 and Cypriots, Syrians, Armenians (http://i.imgur.com/YSkDwzX.png).

Could direct lineal relationship to BR2 relative to direct lineal relationship to Rathlin be higher for Cypriots, Syrians, Armenians than Belorusians, Russians and Germans? Sure. (Though there is likely some noise, as I can't imagine that closely related populations like Belorusians and Poles are really far apart on that).

Alberto said...

Matt, it seems to me we just got into a strange debate here, since I'm not sure we actually disagree about anything fundamental. My comment about that haplotype analysis was:

I think that the haplotype analysis in Cassidy et al. does suggest that BR2 has CHG admixture (actually in a higher CHG/EHG than Rathlin).

Which I still get the same impression, and I don't know if you really disagree with it. And more fundamentally, I think that we agree that BR2 is more or less what is shown by those models using qpAdm and Global 10. Unless you're saying that you think that BR2 is some 17% EHG (or some 30% Yamnaya) as CHG_K8 says, but I don't know if you're arguing that.

Davidski said...

@Matt

If you're wondering why I posted two results each for BR1 and BR2, it's because the program gives output for several different models, and there's practically no difference between the results I posted.

In other words, all four models were produced with the same left and right pops, and there are no significant differences between the statistical fits.

Hence my comment that I think what we're seeing here is the algorithm struggling with Yamnaya Samara because it's an imprecise proxy for the Yamnaya ancestry in these individuals, who probably received their Yamnaya ancestry from much further west than Samara, most likely from somewhere north of the Black Sea.

Davidski said...

Following on from my comment above, I think what we'll soon see as more Yamnaya and closely related steppe samples come in, is the Yamnaya-related portion balloon in groups like Belorussians, Ukrainians and Western Russians that were previously described as having extra WHG ancestry at the expense of Yamnaya ancestry.

Matt said...

@ Alberto:

I don't really think the haplotype analysis really tells you much either way whether BR2 had CHG ancestry or not.

I though it was interesting that qpAdm models with LatviaHG work for BR1 with Yamnaya at around 4% and BR2 at 6%, and which would then infer CHG through that at around 1.5%-2% (if it is 30-40% in Yamnaya / LN1). That could be a poor fit, or not.

I also think it may suggest that ultimately models involving something like Samara_Eneolithic+Latvia_HG/Ukraine_HG+Hungary_CO1 may work better for Hungary_BA than Yamnaya+Hungary_CO1+WHG. Maybe such a mix (Samara_Eneolithic+Latvia_HG/Ukraine_HG+Hungary_CO1) would be also approximated by Western Yamnaya, I have no idea.

Alberto said...

@Matt

I don't really think the haplotype analysis really tells you much either way whether BR2 had CHG ancestry or not.

Maybe you're right. We don't really have enough high coverage ancient samples to really know for sure how good is the correlation between general ancestry and haplotype sharing. I think that with enough samples, there should be some variation, but also some correlation. But I'm only really guessing, I'm afraid.

We'll see when we get more samples if we can figure out with more certainty about BR2-like populations. I think that their shift to the east (compared to MN) will come from a combination of SHG-like and CHG, but if you think it will come more from EHG with no (or little) CHG, then I'll have to consider that possibility as a very real one. Time will tell.