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Friday, October 31, 2014

Genetic continuity and shifts across the metal ages in the Carpathian Basin: analysis of ancient Hungarian genomes CO1, BR1 and IR1


The recent Gamba at el. paper on the genetic prehistory of the Great Hungarian Plain was an excellent piece of paleogenomic detective work. However, I feel that the authors could have done a little better with characterizing the genetic origins of their samples.

For instance, the Principal Component Analysis (PCA) appears to suffer from subtle projection bias, which is a common problem in ancient DNA studies (see here). Also, the model-based analyses, like the ADMIXTURE run, leave me wanting a lot more.

However, all of the samples are freely available online, including in user friendly genotype format at Genetic Genealogy Tools. So I thought it might be useful to take a closer look at three of the genomes, spanning a 2,000-year period from the Copper Age to the Iron Age: CO1, BR1 and IR1.

The metal ages are a critical period of prehistory and early history in the making of modern Europe. It's a time of profound cultural changes, and as we now know, large-scale genetic shifts across the continent (see here). Indeed, the three aforementioned genomes clearly show that major genetic shifts took place on the Great Hungarian Plain from the Copper Age to the Iron Age. However, they also suggest strong genetic continuity in the region throughout this period.

CO1, the Copper Age genome from a Baden Culture burial, appears ridiculously Western European, and could easily pass for a present-day Sardinian in most analyses, even though it's most likely of Balkan and Near Eastern origin. It's very similar in that respect to another Copper Age sample, Oetzi the Iceman from the Tyrolean Alps.

One of the main reasons for this Sardinian-like genetic character is certainly its very low level of Ancient North Eurasian (ANE) admixture, probably much less than five per cent. Almost everyone in West Eurasia has more these days, so they appear a lot more eastern.




Shared drift stats of the form f3(Mbuti;CO1,Test) - Eurogenes dataset

Shared drift stats of the form f3(Mbuti;CO1,Test) - Human Origins dataset



Eurogenes K15 4 Ancestors Oracle results

BR1 represents the Early Bronze Age (EBA) Mako Culture. It looks roughly like a cross between CO1 and someone from northeastern Europe with an unusually high level of hunter-gatherer ancestry, and also a fair whack of ANE. Indeed, after running a variety of tests, I'd say that BR1 has around 12% of ANE (in other words, more than Basques but less than British, which fits with its position on the West Eurasian PCA).

So as far as I can see, the most parsimonious explanation for this result is a population movement into present-day Hungary from the northeast during the EBA, perhaps associated with the early Indo-Europeans and the not-so-pleasant effects of the 4.2 kiloyear event (see here).

Interestingly, the 4A Oracle suggests that BR1 might in large part be a mixture of CO1 and KO1, which is another sample from Gamba et al., assigned to the Koros Culture of early Neolithic Balkan farmers, but with typically hunter-gatherer genetic structure. This opens up the possibility that people with unusually high levels of hunter-gatherer ancestry lived on the Great Hungarian Plain throughout the Neolithic, and the sampling by Gamba et al. was too patchy to find them.

However, it's not possible to get a genome like BR1 simply by mixing CO1 with KO1, because the hunter-gatherer-like sample is not eastern enough. In other words, it lacks ANE. I know this just by eyeballing a couple of PCA, featuring KO1 and Motala12, a Scandinavian sample estimated by Lazaridis et al. to have a ratio of ~19% ANE (see here and here).

So there might well have been a resurgence in local hunter-gatherer DNA on the Great Hungarian Plain, and perhaps throughout much of Central Europe, after the Neolithic. Nevertheless, in my opinion this alone cannot explain the results in this case.




Shared drift stats of the form f3(Mbuti;BR1,Test) - Eurogenes dataset

Shared drift stats of the form f3(Mbuti;BR1,Test) - Human Origins dataset



Eurogenes K15 4 Ancestors Oracle results

IR1, the Iron Age genome, is clearly mixed. In some ways, much like CO1 and BR1, it's also deceptively similar to present-day Western Europeans, which suggests that it's in large part of local origin. However, its uniparental markers (Y-haplogroup N-M231 and mitochondrial haplogroup G2a1) actually fit better in Siberia than anywhere in Europe, and its genome-wide DNA shows influences from the North Caucasus and Volga-Ural regions (refer to the 4A Oracle results below).

Because of its complex ancestry, I can't accurately estimate the level of ANE admixture in this genome. Nevertheless, the PCA and Eurogenes K15 suggest that it easily surpasses BR1 in this respect. Note, for instance, its position among the Kargopol Russians and North Ossetians on the global PCA plot, as well as its high Eastern Euro score in the Eurogenes K15.

What I think this hints at is that the present levels of ANE across Europe aren't the result of a single early Indo-European migration, but multiple population movements around the continent spanning the entire metal ages, although usually involving Indo-European groups, and the effects of isolation-by-distance.

By the way, IR1 comes from a burial site of the Mezocsat Culture, which is generally accepted to be of Cimmerian origin. The Cimmerians are usually described as a nomadic Indo-European people from the Kuban steppe, just north of the Caucasus, who were pushed west by the expanding Scythians. Apparently, they founded a variety of cultures in the Carpathian Basin and Balkans by imposing themselves as the ruling elite over the locals. It's remarkable how closely IR1's genetic structure fits this narrative.




Shared drift stats of the form f3(Mbuti;IR1,Test) - Eurogenes dataset

Shared drift stats of the form f3(Mbuti;IR1,Test) - Human Origins dataset



Eurogenes K15 4 Ancestors Oracle results

Also, here's a really cool map of Identity-by-Descent (IBD) hits of over 3 cM shared between IR1 and a wide range of present-day populations. It comes from a recent post at Vadim's blog (see here). The shared IBD peaks are found in East Central Europe and the Volga-Ural region, which makes sense.


381 comments:

1 – 200 of 381   Newer›   Newest»
Davidski said...

Here are the results for M4 from the Borum Eshøj site, which I think is essentially a Kurgan. Noisy as hell, but clearly the implication here is that this genome has a lot of ANE. I'll try and get more sensible results over the weekend, by maximizing the number of markers.

K15

North_Sea 0
Atlantic 31.88
Baltic 0
Eastern_Euro 28.12
West_Med 0.66
West_Asian 0
East_Med 0
Red_Sea 6.66
South_Asian 0
Southeast_Asian 0
Siberian 9.79
Amerindian 12.72
Oceanian 10.18
Northeast_African 0
Sub-Saharan 0


K13

North_Atlantic 36.4
Baltic 0
West_Med 0.02
West_Asian 17.85
East_Med 0
Red_Sea 13.07
South_Asian 0
East_Asian 0
Siberian 4.34
Amerindian 15.75
Oceanian 12.56
Northeast_African 0
Sub-Saharan 0.01

Helgenes50 said...

Thanks for this remarkable work.

Since you are speaking of IBD, do you think that the tool ONE TO ONE at Gedmatch is really accurate ? because, if it's the case, this tool is very useful to compare our results with those of the ancient genomes

And what are the best settings, 2 or 3 cM and 700 SNPs ?

Davidski said...

I really can't comment about that tool because I'm not familiar with it. But any tool trying to find IBD hits in degraded, fairly low quality ancient samples will have a hard time coming up with accurate results.

Chad Rohlfsen said...

David,
This guy looks like extreme Iranian, or something. Kind of our Yamnaya type, possibly.

Here's the calculator results.
EEF 55.05115328
WHG 29.61674973
ANE 15.33209699

Near East 66.212
ANE 33.788

I think it's going to be reversed a little on the top calculator. Maybe 55/15/30. Basically our Yamnaya like person.

ryukendo kendow said...

@ Chad
Is 'this guy' M4?

Chad Rohlfsen said...

He's positive for S4067. Those S ones fall under R1b for S3025-S6124. I don't see anything that is not R1b between there. It's hard to say. Barak, do you know a good way to search for his snp's?

Chad Rohlfsen said...

Yeah, that's M4. The Bronze Age Dane. He has to be mixing into a population that is way under the modern day 46% EEF.

Chad Rohlfsen said...

Here Barak,

PF141-, CTS1108-, M8978-, Z879-, F1391-, Z12176-, YSC0000122+, YSC0000123+, YSC0000137+, YSC0000138+, Z3268-, YSC0000147+, YSC0000148+, YSC0000149+, YSC0000150+, YSC0000151+, Z14274-, YSC0000160+, Z5390-, YSC0000161+, YSC0000162+, YSC0000163+, Z14055-, PF3467-, M2687-, M6488-, S18522-, M7652-, PR2336-, CTS6669-, F415-, M2327-, S19886-, CTS8912-, Z4287-, F3242-, PF3427-, PR6990-, PR6991-, PR6992-, PR6993-, K5-, Z14772-, Z14798-, Y749-, Z7986-, PR7353-, S7101-, Y1268-, S3136-, S26590+, YSC0000139+, YSC0000140+, PF4871-, S4126-, S4611-, S4183+, S4067+

Chad Rohlfsen said...

Damn, I don't know. Safest bet is R1b or I1. I'm not yet finding any of these on the ISOGG site.

ryukendo kendow said...

IR1's scores: Atlantic, North Sea, East Euro, and West Asian.

I predicted the last three, but not the first; wonder what the 'atlantic' affinity means in this context.

IR2 looks like modern-day hungarians pulled in the direction of Chechens.

IR2 shows the highest peaks in East Central Europe, Volga-Ural, and Iran.

ryukendo kendow said...

@ Chad
Nice.
It seems pretty similar to modern Central-North Euros by that time.

Chad Rohlfsen said...

Danes are now 46/38/16. If he ends up being R1b, it seems more Iranic like. It makes sense, with all the R1b by the Caucasus. He looks more Armenian/Karelian than IR1. If only it wasn't so noisy.

David, Can you do an f3, with him and IR1, using Stuttgart and MA-1, so that we can see who is more Near Eastern and ANE?

ryukendo kendow said...

Also, BR1 scores very close to French Basque in both datasets.

Chad Rohlfsen said...

The YSC snp's fall under J and R1b in that range. Those aren't listed either. Very frustrating! Where can I find a haplogroup predictor?

Chad Rohlfsen said...

David,
Can you post a link to the exact page with IR1's, IBD sharing. I am not seeing it on the link you have, and I can't read it to find the right page. All I see are Stuttgart, Loscbour, and maybe Motala. Thank you!

Davidski said...

Yeah, that's the wrong link, but I can't find the right one now. Anyway, here are the IBD stats for IR1 that were used to make that graphic.

Chuvash 26,02 ---//Confidence: high
Polish 25,03 ---//Confidence: high
Ukrainian-West-and-Center 24,44 ---//Confidence: medium
Belarusian 24,24 ---//Confidence: high
Croatian 24,21 ---//Confidence: very high
Hungarian 24,09 ---//Confidence: very high
Russian-North 23,93 ---//Confidence: very high
Iranian 23,79 ---//Confidence: very high
Finnish 22,68 ---//Confidence: very low
Greek 22,66 ---//Confidence: very high
Ossetian 22,64 ---//Confidence: high
Balt 22,58 ---//Confidence: high
Mansi 22,5 ---//Confidence: medium
Erzya 22,42 ---//Confidence: medium
French 22,17 ---//Confidence: very high
Russian-West 22,12 ---//Confidence: medium
Ukrainian-East-and-Center 22,05 ---//Confidence: medium
Tatar-Crimean 22,01 ---//Confidence: low
Italian 21,97 ---//Confidence: very high
Russian-South 21,47 ---//Confidence: very high
Udmurt 21,25 ---//Confidence: high
Adygei 21,21 ---//Confidence: high
Bashkir 21,11 ---//Confidence: low
Tatar-Kazan 21,01 ---//Confidence: high
Sardinian 20,91 ---//Confidence: very high
Romanian 20,87 ---//Confidence: medium
Basque 20,78 ---//Confidence: very high
Swedish 20,57 ---//Confidence: high
Abkhazian 20,34 ---//Confidence: very high
Georgian 20,29 ---//Confidence: high
Sephard 20,14 ---//Confidence: high
Armenian 19,96 ---//Confidence: high
Saami 19,83 ---//Confidence: high
Karelian 19,67 ---//Confidence: high
Veps 19,66 ---//Confidence: medium
Balkarian 19,6 ---//Confidence: very high
British 19,51 ---//Confidence: very high
Komi 19,42 ---//Confidence: high
Tadjik 19,29 ---//Confidence: high
Uzbek 19,24 ---//Confidence: high
Norwegian 18,86 ---//Confidence: high
Turkmen 18,66 ---//Confidence: high
Bulgarian 18,62 ---//Confidence: high
Nogay 18,48 ---//Confidence: high
Ashkenazi 18,44 ---//Confidence: high
Azerbaijani 18,34 ---//Confidence: high
Turkish 18,32 ---//Confidence: high
Tatar_Lithuanian 18,31 ---//Confidence: very low
Chechen 18,28 ---//Confidence: very high
Kazah 18,27 ---//Confidence: high
Lezgin 17,76 ---//Confidence: very high
Greek_Azov 17,28 ---//Confidence: low
Uygur 16,91 ---//Confidence: medium
Moksha 16,87 ---//Confidence: very low
Estonian 16,76 ---//Confidence: high
Hakas 16,65 ---//Confidence: medium
Kumyk 16,14 ---//Confidence: high
Mari 16,01 ---//Confidence: high
Shor 15,93 ---//Confidence: very low
German-Austrian 15,44 ---//Confidence: very low
Ket 15,1 ---//Confidence: very low
Kirgiz 14,41 ---//Confidence: very high
Selkup 13,63 ---//Confidence: high
Mongol 13,63 ---//Confidence: medium
Dolgan 12,9 ---//Confidence: medium
Altaian 12,69 ---//Confidence: high
Tuvinian 12,22 ---//Confidence: high
Evenk 9,96 ---//Confidence: high
Buryat 9,29 ---//Confidence: high
Yakut 9,28 ---//Confidence: very high
Han-North 7,9 ---//Confidence: medium
Nganassan 6,61 ---//Confidence: medium
Even 5,18 ---//Confidence: medium

ryukendo kendow said...

Anyone care to explain why those figures are so "choppy"?
High IBD with Hungarian, Croatian and Greek, but not Bulgarian or Romanian; polish and ukrainian at the top, but the lowest west Eurasian pop is Estonian. Is this the way IBD generally behaves with aDNA?

Chad Rohlfsen said...

Awesome! Thank you, David! I wish that they had North Germans and Danish. There is supposedly some decent "Thraco-Cimmerian" ancestry among those tribes.

Chad Rohlfsen said...

David,
Just eyeballing those plots of Motala and KO1, it seems that they plot above those with similar levels of ANE, in the North. Motala 19 is above Swedes, KO1 is East of the Basque. Maybe, he is 10-12%ANE.

Chad Rohlfsen said...

A plot with Loschbour, to compare all three, would make it a little easier.

Shaikorth said...

Chad, Srkz posted the IBD test here,

http://forum.molgen.org/index.php/topic,7459.195.html

but be warned that it's in Russian and David already posted the total sharing numbers so all info is already here. The Iron Age sequence used in it is the one Felix prepared, I think everyone's using them these days (except Genetiker?).

Chad Rohlfsen said...

Huge news guys! Here is my correspondence with David Reich, after sending him my data.

Dear Chad,


Thanks for your very kind email.


We are working on these types of issues quite hard and have been developing new methodology to look at these issues. Please wait a couple of months until we post our paper on the biorXiv and then you can compare your inferences to our ours.



I agree that the Samara Yamnaya population is not a realistic direct source population for putative migrations from the east to Europe, but it is all we have from the Russian steppe right now and might be related to the source populations.



Yours,
David

And the following e-mails.


Dr. Reich,


Thank you for your response. Are you leaning towards a hunter bounce back, a high WHG western steppe source, or a mix of both? It seems the level of i2 and u5 point to more localized bursts in native hunters. I could be wrong though.





Thanks,


Chad



Dear Chad,



I’m sorry, I don’t feel like I am confident enough in what we’re doing to discuss until we have a paper to submit.



Yours,

David


The last e-mail I sent, suggested IBD testing KO1 with Hungarians and Blatterhohle hunters with Germans. Whether or not that would be fruitful, I don't know. I am still waiting on a response.


Chad Rohlfsen said...

Either he does not want to tip his cap, or he has some serious doubts about us being Yamnaya derived in any great amount. They must look way too Near Eastern, for their taste.

If it ends up not being Yamnaya, the IE homeland better stretch towards Central Europe, or our actual IE ancestry is possibly more mid-late Bronze. Maybe we have some R1 tribes stretching towards Central Europe, who do not speak IE.

Chad Rohlfsen said...

Or, the first R1a and R1b into Europe are way more WHG than ANE, as BR1 would indicate, assuming there isn't much Mesolithic survival. This has to be pretty maddening for them, as they are looked at to have all the answers.

Srkz said...

KO1. Filthering settings are equal to IR1 (but very weakened compared to modern samples, LBK/Stittgart and Loschbour). I also plan to draw BR2 map when Chandrakumar's files will be ready.
http://s017.radikal.ru/i410/1410/71/8883b786cf79.png
Balt 34,53 ---//Confidence: high
Polish 34,16 ---//Confidence: high
Estonian 33,38 ---//Confidence: high
Russian-South 33,19 ---//Confidence: very high
Karelian 33,09 ---//Confidence: high
Belarusian 32,59 ---//Confidence: high
German-Austrian 30,72 ---//Confidence: very low
Norwegian 30,66 ---//Confidence: high
Russian-North 29,65 ---//Confidence: very high
Ukrainian-West-and-Center 29,25 ---//Confidence: medium
Russian-West 28,73 ---//Confidence: medium
Hungarian 28,72 ---//Confidence: very high
Swedish 28,43 ---//Confidence: high
Komi 28,12 ---//Confidence: high
Erzya 27,65 ---//Confidence: medium
Ukrainian-East-and-Center 27,46 ---//Confidence: medium
British 27,17 ---//Confidence: very high
Moksha 26,9 ---//Confidence: very low
Saami 26,64 ---//Confidence: high
Mari 26,14 ---//Confidence: high
Veps 25,99 ---//Confidence: medium
Italian 25,06 ---//Confidence: very high
Finnish 25,02 ---//Confidence: very low
Croatian 24,96 ---//Confidence: very high
Tatar-Kazan 24,24 ---//Confidence: high
Greek 23,99 ---//Confidence: very high
Basque 23,74 ---//Confidence: very high
French 23,71 ---//Confidence: very high
Tatar_Lithuanian 23,68 ---//Confidence: very low
Bashkir 23,66 ---//Confidence: low
Udmurt 23,25 ---//Confidence: high
Chuvash 21,22 ---//Confidence: high
Ashkenazi 20,17 ---//Confidence: high
Sardinian 19,78 ---//Confidence: very high
Adygei 19,76 ---//Confidence: high
Greek_Azov 18,84 ---//Confidence: low
Mansi 18,44 ---//Confidence: medium
Bulgarian 18,26 ---//Confidence: high
Romanian 18,04 ---//Confidence: medium
Kumyk 17,97 ---//Confidence: high
Uygur 17,33 ---//Confidence: medium
Chechen 17,05 ---//Confidence: very high
Turkish 16,71 ---//Confidence: high
Sephard 16,62 ---//Confidence: high
Balkarian 16,5 ---//Confidence: very high
Tatar-Crimean 16,19 ---//Confidence: low
Uzbek 15,86 ---//Confidence: high
Abkhazian 15,84 ---//Confidence: very high
Tadjik 15,52 ---//Confidence: high
Kirgiz 15,18 ---//Confidence: very high
Armenian 14,84 ---//Confidence: high
Ossetian 14,77 ---//Confidence: high
Turkmen 14,71 ---//Confidence: high
Nogay 14,52 ---//Confidence: high
Georgian 14,13 ---//Confidence: high
Azerbaijani 13,81 ---//Confidence: high
Ket 13,79 ---//Confidence: very low
Kazah 13,24 ---//Confidence: high
Lezgin 13,15 ---//Confidence: very high
Dolgan 12,69 ---//Confidence: medium
Selkup 12,44 ---//Confidence: high
Iranian 12,41 ---//Confidence: very high
Hakas 12,05 ---//Confidence: medium
Altaian 11,49 ---//Confidence: high
Shor 9,85 ---//Confidence: very low
Mongol 8,9 ---//Confidence: medium
Yakut 8,06 ---//Confidence: very high
Tuvinian 7,6 ---//Confidence: high
Han-North 7,03 ---//Confidence: medium
Nganassan 6,76 ---//Confidence: medium
Evenk 6,22 ---//Confidence: high
Buryat 5,93 ---//Confidence: high
Even 5,73 ---//Confidence: medium

Srkz said...

"The shared IBD peaks are found in East Central Europe and the Volga-Ural region, which makes sense"
Not only the Central Europe and Volga-Ural, but also Iranic-speaking Ossetians in the North Caucasus (Ossetian spot was blurred by neighbors)

Srkz said...

"Confidence" means sample size:
1-4 very low
5-9 low
10-14 medium
15-19 high
20 and more very high
BR2 should be less noisy

Chad Rohlfsen said...

Any chance you could do BR1 and M4? Thanks!!

Srkz said...

I've done BR1, but i think it is very noisy, even compared to IR1 and KO1. No chance for M4, it just don't have enough SNP's
http://i003.radikal.ru/1410/65/899618216c74.png

Finnish 59,39 ---//Confidence: very low
German-Austrian 53,21 ---//Confidence: very low
Swedish 51,65 ---//Confidence: high
Polish 50,69 ---//Confidence: high
Belarusian 50,36 ---//Confidence: high
Hungarian 49,87 ---//Confidence: very high
British 49,2 ---//Confidence: very high
Russian-South 48,96 ---//Confidence: very high
Russian-North 48,88 ---//Confidence: very high
Russian-West 48,18 ---//Confidence: medium
Ukrainian-West-and-Center 47,67 ---//Confidence: medium
Balt 47,27 ---//Confidence: high
Croatian 47,2 ---//Confidence: very high
Erzya 46,98 ---//Confidence: medium
Ukrainian-East-and-Center 46,69 ---//Confidence: medium
Estonian 46,5 ---//Confidence: high
Komi 46,02 ---//Confidence: high
Basque 45,76 ---//Confidence: very high
Moksha 45,36 ---//Confidence: very low
Bulgarian 45,19 ---//Confidence: high
Karelian 44,51 ---//Confidence: high
French 44,39 ---//Confidence: very high
Norwegian 43,71 ---//Confidence: high
Veps 43,15 ---//Confidence: medium
Sardinian 42,98 ---//Confidence: very high
Italian 42,13 ---//Confidence: very high
Romanian 41,8 ---//Confidence: medium
Ashkenazi 41,76 ---//Confidence: high
Tatar-Kazan 41,7 ---//Confidence: high
Kumyk 40,29 ---//Confidence: high
Greek 39,99 ---//Confidence: very high
Udmurt 39,54 ---//Confidence: high
Ossetian 39,16 ---//Confidence: high
Greek_Azov 38,82 ---//Confidence: low
Chechen 38,33 ---//Confidence: very high
Tatar-Crimean 38,25 ---//Confidence: low
Balkarian 37,98 ---//Confidence: very high
Chuvash 37,84 ---//Confidence: high
Bashkir 37,82 ---//Confidence: low
Turkish 37,71 ---//Confidence: high
Mari 36,27 ---//Confidence: high
Tadjik 35,83 ---//Confidence: high
Nogay 35,73 ---//Confidence: high
Abkhazian 35,41 ---//Confidence: very high
Saami 35,01 ---//Confidence: high
Adygei 34,36 ---//Confidence: high
Sephard 33,89 ---//Confidence: high
Armenian 33,74 ---//Confidence: high
Iranian 32,76 ---//Confidence: very high
Azerbaijani 32,75 ---//Confidence: high
Lezgin 31,84 ---//Confidence: very high
Turkmen 31,08 ---//Confidence: high
Uzbek 29,72 ---//Confidence: high
Georgian 29,63 ---//Confidence: high
Kazah 28,56 ---//Confidence: high
Mansi 27,48 ---//Confidence: medium
Uygur 26,01 ---//Confidence: medium
Altaian 24,83 ---//Confidence: high
Shor 23,64 ---//Confidence: very low
Hakas 22,37 ---//Confidence: medium
Kirgiz 22,31 ---//Confidence: very high
Tatar_Lithuanian 20,26 ---//Confidence: very low
Ket 19,66 ---//Confidence: very low
Dolgan 19,42 ---//Confidence: medium
Selkup 17,7 ---//Confidence: high
Mongol 13,39 ---//Confidence: medium
Buryat 13,2 ---//Confidence: high
Evenk 12,45 ---//Confidence: high
Tuvinian 12,41 ---//Confidence: high
Han-North 12,08 ---//Confidence: medium
Nganassan 12,06 ---//Confidence: medium
Yakut 10,63 ---//Confidence: very high
Even 7,69 ---//Confidence: medium

Chad Rohlfsen said...

The great population explosion happened in Southern Germany and Austria, so that makes sense. Hungarians and Brits top the very high confidence. Interesting.

MfA said...

Iranian scores might be higher if afro-iranian and iranian arabs had been removed in behar et al. samples. How about using more homogenous Yunusbayev et al. Kurdish samples instead?

Grey said...

"IR1's scores: Atlantic, North Sea, East Euro, and West Asian. I predicted the last three, but not the first; wonder what the 'atlantic' affinity means in this context."

Standard Euro WHG but with a trace of N/NW African.

(just a guess)

.

"Or, the first R1a and R1b into Europe are way more WHG than ANE"

If there was a transition zone between farmer and steppe then the people in the transition zone with a half IE package might have been the first to be displaced by people fully on the steppe with the full IE package.


Chad Rohlfsen said...

Atlantic is more EEF like and less ANE like than North Sea. It's got nothing to do with Africans.

Eduardo Pinto said...

This would be an insightful exercise to reproduce with K15/K13 and ANE_K7


"Inter-relationships between Dodecad K7b and K12b components"

http://dienekes.blogspot.pt/2012/09/inter-relationships-between-dodecad-k7b.html

ryukendo kendow said...

@ Chad
Could you do some analysis of the components in the k15 calculator through the EEF WHG ANE tests as well? The figures in k13 are nice, but I have a feeling that k15 segregates the three pops more cleanly than k13 does.

K15 certainly seems to segregate cleanly into ancient DNA, so this might help add to my admittedly very shallow analysis below.

Some observations.
1) The Neolithic individual CO1 is dominated by Atlantic and West Med, in an approx 2:3 ratio.

BR1 is dominated by the same, with the addition of Baltic and North Sea. It is interesting to note that the ratio of Atlantic to West Med in BR1 is the same ~2:3 as in CO1. Baltic and North sea are close to 1:1.

IR1 has all the above four, with the addition of East Euro and West Asian.

It appears, from the all the analyses we have now, that Atlantic and West Med are the primary neolithic components, and the WHG in these components are segregated from that in Baltic, prob pointing to an early admixture of pure basal neolithics with WHG somewhere in the Med to produce EEF.

In BR1, Baltic probably represents WHG survival in HG populations into the Neolithic. North Sea seems to represent the mixed WHG+ANE intrusion into HGs from an early time.

If we accept IR1 as similar to a prototypical Kurgan, then these figures are it. If we accept IR1 as a kurganized individual, then the new intrusive components, East Euro and West Asian, are probably the things to focus on. Also, notice that he has low West Med, putting a floor on how much Basal he might have gotten from the Sardinian-like EEF in Europe.

IR1 also differs by having North Sea ~2X higher than Baltic, and Atlantic ~4X higher than West Med, when the former two are 1:1 in BR1 and the latter two are 2:3 in the neolithic individual; this means that he cannot be merely BR1+CO1+West Asian+East Euro. The intrusive element must also contain a some North Sea and quite a bit of Atlantic, with little Baltic and West Med, so the ratios change.

I'm not sure how to interpret this; North Sea might mean some small slice of his ANE+WHG came from the WHG+ANE HG pop in europe. Atlantic is just weird.

ryukendo kendow said...

@ Chad @ Davidski
Your analyses of M4 contradict. Chad implies very high EEF, David implies almost no EEF.

Hope we get the noise out.

ryukendo kendow said...

Addendum to my previous comment.
High north Sea and atlantic with low baltic and low West Med can be found far to the northwest of Europe, in the isles. Some of the Hinxtons are examples.

So IR1 is more "Northwestern" than predicted, especially with regard to his high WHG components. Why though?

Chad Rohlfsen said...

I'm going by the calculator scores on the K13. I think that David just said it has a lot of ANE. I agree with that assessment. No doubt. He is probably over 20%ANE.

Chad Rohlfsen said...

His EEF in k15 depends how much EEF is in the Atlantic component. It would take me a damn long time to figure out the approximations of each. The thing about k13, is that it's built in to figure out if you make someone 100% of a component.

Grey said...

"Atlantic is more EEF like and less ANE like than North Sea. It's got nothing to do with Africans."

If both EEF and some WHG have an African trace might that not confuse the signal between them?

"Atlantic and West Med are the primary neolithic components, and the WHG in these components are segregated from that in Baltic, prob pointing to an early admixture of pure basal neolithics with WHG somewhere in the Med to produce EEF."

Another thought is there's a difference between the Atlantic megalith form of EEF and the rest and that difference is mirrored in a component of IR1 i.e. it's not actually "atlantic" but looks like it?

ryukendo kendow said...

@ Chad
Thanks for the answer.

So the huge EEF figure came from West Asian and Red Sea?

Chad Rohlfsen said...

Red Sea
EEF 113.5571898
WHG -16.85837478
ANE 3.301184967

West Asian
EEF 88.75184039
WHG -2.440100982
ANE 13.6882606

North Atlantic
EEF 36.09902375
WHG 46.76502641
ANE 17.13594984

Grey said...

"a difference between the Atlantic megalith form of EEF and the rest"

should have been

"a difference between the atlantic megalith form of farmers and the rest"

ryukendo kendow said...

@ Chad @ David
That's kinda difficult to reconcile with the k15.
The k15 results might look very different without the noise.

Chad Rohlfsen said...

It's noisy. We'll just have to wait for David to clean it up.

Davidski said...

I don't think KO1 has any ANE. It's just a less extreme version of Loschbour. You can compare the two...

https://drive.google.com/file/d/0B9o3EYTdM8lQdkJXZF9BSFdsRk0/view?usp=sharing

https://drive.google.com/file/d/0B9o3EYTdM8lQYTE4X1U2V3Rmb1k/view?usp=sharing

CO1 might have a couple per cent of ANE, like most Sardinians do. But it's actually much younger than the first suspected Yamnaya-related movements into the Balkans of the Suvorovo Culture.

https://www.academia.edu/3535020/Two_IE_phylogenies_three_PIE_migrations_and_four_kinds_of_steppe_pastoralism

So all of the ANE in East Central Europe is probably related to the Indo-European expansions.

By the way, it sounds like we'll see the new paper at bioRxiv at Xmas time, like last year. That's good, because M4 doesn't offer enough markers for proper testing, so IR1 will be the closest thing we'll have to Yamnaya for a while IMO.

Chad Rohlfsen said...

David,
Check this out!

http://www.cell.com/ajhg/abstract/S0002-9297(14)00427-3

Davidski said...

I reckon this is better for ancient genomes, but it'd take me time to set it up.

http://biorxiv.org/content/early/2014/07/15/003988

Chad Rohlfsen said...

Nice! Yeah, it would be interesting to see some runs, with ancient genomes.

ryukendo kendow said...

@ Davidski
I'm not sure that is the best interpretation. If we draw a vector from CO1 to modern day Hungarians, or from CO1 to IR1, and use either of these as the IE vector, neither can bring us from CO1 to BR1.

In fact, we can only get from CO1 to BR1 if the input vector were something like Motala in the pca.

On the other hand, if we use Sardinian as EEF, a vector from sardinian to BR1 gives us CO1 (and also French Basque), and a vector from BR1 to IR1 gives us present-day Hungarians; but these two are not the same vectors.

Of course we might be best able to confirm this if all the samples were in a single pca.


Chad Rohlfsen said...

David,
I don't know about the PCA plots. Loschbour and KO1 make the other populations move around differently. Can you do an f3
Loschbour Mal'ta KO1
or even Loschbour Motala12 KO1?

barakobama said...

What specific location do the Tatars and Maris in K15 come from?

Davidski said...

Here's a PCA with all three.

https://drive.google.com/file/d/0B9o3EYTdM8lQXy1fbWd5RkpxQ1U/view?usp=sharing

Forget it. Modern North/Central/East Europeans simply don't exist without massive migrations from the steppe.

This is obvious in everything we've seen so far. It can't be any more obvious than it is.

Btw, I have no idea where these Tatars and Maris are from. Probably from the Mari Republic and Tatarstan near the Volga.

ryukendo kendow said...

@ Davidski
Thanks! Could you also include BR1 and IR1 in the plot?

"Forget it. Modern North/Central/East Europeans simply don't exist without massive migrations from the steppe."

Nobody is denying that. The issue is what else has also entered into the formation of European genomes.

East Europeans cannot be the product of a neolithic population mixed with something that is 50% Armenian and 50% something else, whatever that is. The exxtremely high WHG must come from something else, like a BR1-like pop or something similar.

Neither the Bronze Age Dane nor IR1 have high enough WHG to pull so far northeast, and BR1 prob does not have enough ANE to qualify as an IE elite individual.

Chad Rohlfsen said...

That's crazy looking. I am still curious about doing the f3, and maybe doing one with La Brana and Motala12, for comparison.

I think that Reich is still on the fence about how we got our WHG. Apparently they are trying to figure out if it is Mesolithic survival, a source that is between Neolithic Europe and Yamnaya, or a mix of both, with some Yamnaya on top. He doesn't seem confident on Yamnaya, anymore. I am pretty damn curious about the Pit-Combed Ware, Dnieper Don, Bug-Dniester, and Kemi Oba groups. I suppose it could be possible for a population between Central European farmers and Yamnaya to be in the ballpark of 20/60/20, or 10/70/20, 10/60/30. I think they have come across the same numbers as myself, and don't like making a huge survival assumption, without any data to back it up. I am betting they wish that they could withdraw that statement of Corded Ware being 73% Yamnaya. Just because something can be modeled someway, doesn't mean that it is. I am betting that 27% was WHG, and now they have to backtrack.

Chad Rohlfsen said...

David,
Perhaps you can try and mix some things together and see what you get. I am thinking CO1/Oetzi, Motala12/Estonian, IR1.

To be exact, to make the first sample, if you can combine the snps of CO1, mix in a Motala/Lithuanian or Estonian hybrid, and then IR1. I would say mostly the Copper Age samples, with the hunters, and then throw in what you can from IR1. It doesn't have to be a lot. I wonder if that would plot with BR1.

If you prefer, do it in layers. First see where a copper and hunter mix lands. Then, where it goes with some extra ANE from IR1, and even a few snps from M4, if you fancy it.

Davidski said...

Pitted Ware probably came to Scandinavia from Eastern Europe, so they were the early precursors of the Indo-Europeans. Via a different route though.

Anyway, here's a plot of CO1, BR1 and KO1.

https://drive.google.com/file/d/0B9o3EYTdM8lQQVJTQ0dTU0ZLdE0/view?usp=sharing

Quite clearly, BR1 has some eastern stuff that wasn't in the Carpathian Basin before. This is probably linked to the expansions of the Corded Ware and Unetice Cultures. Oh, and I suspect they were Indo-Europeans.

ryukendo kendow said...

@ Chad
Once we have included Loschour, CO1, IR1, BR1 into the dataset, I have a feeling that a vector from CO1 to IR1 would end up reaching Hungarian.

A vector from CO1 to French Basque in the above PCA ends up reaching french, so this is significant I think. This vector is basically horizontal and, if extended for long enough, ends up where David's PIE Frankenstein was located.

Probably a high-WHG pop resembling KO1 or BR1 created a series of Basque-like pops with higher WHG out from a Sardinian-like neolithic, of which CO1 was a partial representative (there might be other pops with even higher WHG). And then the result was Kurganized to create modern European populations.

It is also instructive that IR1 shares the least IBD in west Eurasia with Estonians, and estonians form the most northerly pop in the PCA, away from IR1.

ryukendo kendow said...

@ Davidski
Thanks!
Sorry for the reposts, but could you include IR1 in the plot?

Davidski said...

Yes, here...

https://drive.google.com/file/d/0B9o3EYTdM8lQSDQxRklQc1NaX28/view?usp=sharing

This is why I usually don't run ancient genomes together.

ryukendo kendow said...

Lol!
Why is this genome the only one to behave in this way? The others score reasonably close to where they score individually.

Davidski said...

IR1's not the problem. Having all four ancient genomes on the same plot is the problem.

In any case, you can see that at the EBA stage of proceedings (BR1's time) there are signs of gene flow from the east into Central Europe, and this is already after the initial Yamnaya and Corded Ware expansions.

IR1 comes from the post-PIE steppes, so it's still a useful sample as far as the making of modern Europe is concerned, but it's not very informative about the PIE populations that pushed west during the Copper Age.

ryukendo kendow said...

@ Davidski
I agree with you that ANE probably entered Europe with PIE. But this does not mean all ANE in Europe is due to PIE, or that when there is ANE, then it must be IE.

Basques have more ANE than Sardinians, but Basques are non-IE while Sardinians are. And Motala is insufficient to produce ANE in some individuals, but that does not mean that it never introduced ANE in any individuals in old Europe. If some ANE came from Motala, then the eastward shift will be seen too.

So far we have four datapoints that have a probability of being IE. 1) Yamnaya, which we know are 50% Armenian + 50% Karelian, high Basal, high ANE. 2) Bronze Age Dane, very high EEF, very high ANE, membership in East Euro in ADMIXTURE. 3) IR2, high EEF, high ANE, membership in East Euro in ADMIXTURE. 4) BR1, low ANE, low EEF, very high WHG, basically no membership in East Euro in ADMIXTURE. I think you would agree with me that the most dubious case both archaeologically and autosomally is the last one.

He might be IE, he might not, difficult to say. My reasoning for him not being IE is 1) He strikes me as the kind of individual that can only be produced after introgression over a number of generations only, and 2) this introgression must have occurred with Hunter-Gathers for basically every single generation with the IE elite, which is a weird scenario to say the least.

barakobama said...

"Basques have more ANE than Sardinians, but Basques are non-IE while Sardinians are. "

They're as Indo European-Italian as French are Roman.

barakobama said...

Or as Davidski is English.

Davidski said...

Basques are in all likelihood more Indo-European genetically than those Sardinians from the HGDP.

Also, M4 is really not a useful datapoint, and the Yamnaya groups from the Samara probably aren't the ones who pushed into Europe, but into Asia.

ryukendo kendow said...

@ Davidski
Who were the cultural progenitors of and the largest autosomal contributor to Corded Ware?
Yamnaya.

We know this for a fact. What we do not know is how much Corded Ware contributed to genomes today.

@ Barak
That is a meaningless statement. Is IE a linguistic or a genetic demarcator?

Mike Thomas said...

I still can't believe how so many otherwise intelligent people are imaging of things a "genetically Indo-European". From wherever it came from, and when, the adaptation of IE speech by the individual communities and chiefdoms of Bronze Age Europe was a complex sociolinguistic affair involving active choice, bilingualism, rejection, etc; and not really about the speculative movements we are attempting to model on the basis of still rather preliminary data.

Really, Im at a loss at some of the thought processes here....

Tesmos said...

Davidski,

Which populations do you consider as Northern Europeans that could have not exist without the the migrations from Eastern Europe?

ryukendo kendow said...

@ MT
Bryan Sykes tried to prove Cavalli Sforza wrong about demic change during the neolithic. But Sykes' 'thought process' was disproved.

Demic intrusion with culture and language is common. They are in concordance all over the place. Looking at history, there was probably very little 'active choice' in the matter.

Matt said...

@ Davidski - That PC with KO1, CO1 and BR1 run together with moderns is interesting, since the ancient Hungarians all really seem to move in a KO1 direction.

I'm wondering whether it is due to some Hungarian hunter gatherer specificity (and specific contrast with West Asia and the Near East) of descent coming out strongly in that plot. E.g. PC1 and PC2 are beginning to transform into a PC of ancient Hungarian HG vs modern Near East and West Asia.

Or is it more because of more general European HG to ancient Hungarian links which are obscured in modern PCA because of less direct relationships or something (e.g. samples with high mixes of EEF and WHG don't really exist very much in the modern day, the Basques being the closest relation, so the PCA has a hard time making a “proper” EEF-WHG axis that doesn't suffer from projection bias).

Or some characteristic of how these ancient samples were sampled (e.g. for particular SNPs, which are less variable between them and vary more between them and the other samples).

One point of interest in this direction would be that it does seem like modern Hungarians from Hungary also move “Northwest” on the graph a little, relative to other populations. Not much, but unless my eyes deceive... That suggests some local effect.

Like I would ask if Loschbour, Oetzi and Bronze Age Hungarian 1 generate essentially the same plot, and whether BR1 sits more centrally on that (compared to this ... but I'm sure that would be impossible due to overlap.

Matt said...

Another angle – why does KO1 seem closer to modern Europe than Loschbour, or La Brana?

One answer could be farmer mixture into KO1 and that's plausible, since he(?) is in an early Neolithic context.

The other could be that KO1, compared to Loschbour, happens to be more closely related to both the Near Eastern hunter gatherers who contributed to EEF, *and* the Eastern European hunter gatherers who contributed to Indo-European (or at least its manifestation in Europe).

These are the hunter gatherer ancestors who contributed substantially and widely across Europe, rather than narrowly or weakly to the present day populations from their local region.

I guess relatedness to East Asian and African outgroups relative to Loschbour and La Brana would explain this, by showing whether KO1 had basal eurasian, therefore farmer ancestry, or didn't, in the proportions to explain this.

Davidski said...

None of the present-day ethnic groups in Europe would exist today in their current form if not for this post-Neolithic wave from the east.

Only the Basques kept their language, probably because they were high up in the hills in far Western Europe. But it's clear that they were also affected by the gene flow from the steppe, because they're very different from Copper Age Europeans like Oetzi and CO1.

However, the fact that the Basques kept their language and culture is probably why they were spared from the affects of the later waves from the east, like the Iron Age expansions into Europe of the Cimmerians and such (ie. IR1's relatives). Note that most Spaniards do show the West Asian/Caucasian type of ancestry, because they have always been part of the European mainstream, unlike Basques.

Davidski said...

Btw, yes, it's a good bet that KO1 is part farmer. Its archeological context is farmer not hunter.

ryukendo kendow said...

@ Davidski
I suppose the Cimmerians and the Bronze age collapse must have reached Orcadians off scotland and west Irish and Norwegians in their fjords, while avoiding Basques?

Really, David, the evidence is simply incontrovertible that some time of Near-East/Caucasus-like ancestry was carried in the PIE population. It might not make up the majority of the population; it might simply make up some fraction. The Yamnaya were already mentioned to be part caucasus/near east, which means the Corded Ware must have it, and now we have IR1 and possibly the Bronze Age Dane as well. What makes this so difficult to admit?

Davidski said...

Ask yourself where the ancestors of present-day Norwegians and Orcadians were during the Bronze and Iron Ages. And I mean all of their ancestors, not just the Celts, Germanics, but also German migrants to Norway, etc.

Then compare them to the Basques, who've been isolated in the Pyrenees since the Bronze Age. And then you shall have the answer to your question.

Oh, by the way, there are indeed plenty of legends of late steppe groups making it all the way to places like Uppsala in Sweden. But even if these aren't true, my point obviously still stands.

ryukendo kendow said...

@ Davidski
Was it more conducive for a fleeing mycenean to end up in the baltic taiga, than for him to end up in Basque county? I suppose these escaping migrants from the steppe and the Bronze age collapse account for all the West Asian in the Spanish or British population vis-a-vis Basque? So Scythian/Cimmerian and Mycenean refugee input accounts for a sig slice of contribution to Orcadian and West Irish, and is sufficient to distinguish Spanish from Basque? This is hardly plausible.

The ancestors of Germans and Celts were wherever they were. They just got their Caucasus/West Asian input from Corded Ware, which was already significant in Yamnaya, as the paper will state.

The point is, did the PIE population carry caucasus and near-east specific ancestry, or no?

Richard Rocca said...

@ryukendo kendow said..."Basques have more ANE than Sardinians, but Basques are non-IE while Sardinians are."

Sardinians spoke a dead non-IE language up until the Roman period. Paleo-Sardinian and Proto-Basque likely originated from a common language (Balsco-Ferrer 2013), likely from the Copper Age. Sardinia, Basque country and the pre-Roman area of the "Iberians" which spoke a Basque-like language all have a spike in I2a-M26 not found anywhere else in Western Europe.

@Davidski said..."Btw, yes, it's a good bet that KO1 is part farmer. Its archaeological context is farmer not hunter."

Of caution about the archaeological context of KO1 being a farmer from one of the authors of the paper:

"The archaeological information isn't enough to say whether he was married to a local farmer, said Ron Pinhasi, an archaeologist at University College Dublin and co-author of the new study. It may even be that the man's skull was a trophy of some sort, Dr. Pinhasi added.

Chad Rohlfsen said...

Yamnaya should go the way of the dodo bird. If Reich doesn't like it, we should look for something intermediary. No one really comes off as yamnaya, except maybe ir1 and m4. Between Samara and CT, things must be pretty different.

barakobama said...

"I still can't believe how so many otherwise intelligent people are imaging of things a "genetically Indo-European"."

Come one Dude. There's no need for skeptic speechs, which go now where because they're skeptical of all ideas. We have a pretty good idea who the people were that brought Indo European languages to most of Europe were.

I can't mention every 1,00,000.... possibilities in one post. Just because I say there are Indo European genetic markers doesn't mean I'm a die-hard believer, it just means I think that's most likely true.

I get your point but the days of old-school skeptics of populations genetics are over. People are really discovering stuff that goes along with archaeology and history, that no reasonable person can deny.

Sardinians have spoken Italian and Latin languages, despite being very different genetically to mainland Italians. French and Spanish speak a derivative of Latin and yet are not very Italian at all, Davidski and Ryk speak English but are not very English at all, etc. Sardinians speaking an Indo European language(since Roman times only!) means almost nothing. They're practicality 90%> Neolithic relics, they have very little Indo European blood, END OF STORY.

Chad Rohlfsen said...

"I agree that the Samara Yamnaya population is not a realistic direct source population for putative migrations from the east to Europe, but it is all we have from the Russian steppe right now and might be related to the source populations"

David Reich

I think that we should find something that is between CO1 and extreme Mesolithic survival, being mixed with something between that Motala and Yamnaya. That is probably the people that created our Bronze Age ancestors.

Considering population explosion at this time, if could be safe to assume that those two provide much of our ancestry, with later Bronze and Iron Age individuals being more of the Near East/ANE mix (true Samaran type). For instance, a 20-40% Mesolithic survival, and an invasion of people that are around 20-40%EEF. There is really no way to know without many more samples and comparing the size of hunter camps with farming communities, in the late Neolithic.

Chad Rohlfsen said...

Granted, they may be Indo-European speaking, but are greatly influenced genetically, by the hunters already residing there. If Indo-European is more ANE driven, then they can still speak it, through more of an elite dominance, than genetic dominance.

barakobama said...

Is there a way to make a EEF-WHG-ANE calculator with K15? Maybe the exaggerated WHG in Iberians is due to North Atlantic, which kind of gets split between North Sea and Atlantic in K15.

Chad Rohlfsen said...

Lazaridis had them with decent amounts of WHG too. It's not the calculator's fault.

Chad Rohlfsen said...

I am wondering if that African admixture is making Western Iberians more EEF than they really are.

It might only be a percent of two though.

Eduardo Pinto said...

@Barak

IMO contemporary Iberians have elevated WHG levels because we got it from three different sources, namely:

- Middle Eastern HGs through maritime seafaring agriculturalists

- North African HGs through North African farmers - who were responsible for the spread of the farming movement in the western portion of Iberia -

- Native HGs of Atlantic affiliation


You can also add a fourth, though a minor one, IE-affiliated movements into Iberia during the Iron age.




@Chad

The African admixture is contained in the Eastern African cluster not in the ENF one.

Mike Thomas said...

@ B O'Bama

"Sardinians speaking an Indo European language(since Roman times only!) means almost nothing. They're practicality 90%> Neolithic relics, they have very little Indo European blood, END OF STORY"

Perhaps yes to the former, but there was no IE blood, so I disagree with the latter qualifier. I'd say they have little of the new Bronze Age , eastern-shifted input.

Chad Rohlfsen said...

Edward,
There isn't an African component in the EEF / WHG / ANE calculator. It elevates the EEF.

barakobama said...

That eastern blood was brought mostly by IE speakers. So, saying Sardinians are Indo Europeans but have less than non-Indo European Basque means nothing, it's a miss leading statement.

The people who spread IE in bronze age Europe had ancestry, and we have a pretty good idea what their ancestry was. Saying there's no genetic markers from the IE-spread is plain false. I know it's an attempt to be a scientist but sometimes you have to openly say what's most likely and not only doubt about things.

barakobama said...

Eduardo, you can use the K13 EEF-WHG-ANE calculator and put African components in Iberians to 100, to see what they score, and see if they would raise WHG. I guess some North African-WHG like blood could be expressed in more complex ways though.

Near eastern-WHG doesn't go into Laz WHG. This is because Stuttgart's near eastern ancestors had less WHG than her and modern near easterns have far less, so it wouldn't add to the Laz WHG score.

Grey said...

"I am wondering if that African admixture is making Western Iberians more EEF than they really are.

It might only be a percent of two though."

There's known connections between Atlantic Megalith and NW Africa and as you say it might only be a percent or two but I do wonder what the effect might be if any.

.

"Sardinians ... have very little Indo European blood, END OF STORY"

It seems to me Sardinia may have been kind of vaccuum sealed by coastal malaria and could contain lots of clues.

Grey said...

Similarly I wonder about some Inuit-like mixture influencing the Baltic from the north - again not much but maybe enough to confuse things.

Davidski said...

Eduardo,

The reason that southwest Europeans show more WHG in the EEF/WHG/ANE calculator than they should is basically because the calculator works on the assumption that EEF, WHG and ANE are as clinal in their frequencies across Europe as the components from the K13 test.

But this is not true, because relatedness to Stutgart rises sharply in southwestern Europe, and thus so does EEF, while the West Med component from the K13, which shows the greatest correlation with EEF, not so much.

Mike,

The early Indo-European speakers carried very specific unipaternal and genome-wide markers, and they spread these deep into Europe during the Copper Age. That's what Barak means by "IE blood".

It's possible to track migrations with genetic markers. The Indo-European migration is no different in this respect.

Grey,

There are a number of populations in Europe that violate the EEF/WHG/ANE model because of minor and no so minor post early Indo-European admixture events in Europe, and these cases are discussed in Lazaridis et al.

Davidski said...

rk,

The point I'm making is that there might be different reasons for the current frequencies of the various West Asian/Caucasus components in Europe today than the Proto-Indo-European expansions.

The fact that the Basques and many Sardinian groups have not been part of the European mainstream from the Bronze Age onwards really looks to me like the best explanation available. Claiming that Orcadians and Norwegians can be compared to these two groups is wrong, and you can see that in any half decent analysis, which shows that Basques and the HGDP Sardinians are outliers from the European mainstream, while Orcadians and Norwegians not nearly as much.

So the West Asian/Caucasus components can't be used to track the early Indo-European expansions. They can only be used to pinpoint post-Bronze Age linguistic, cultural and geographic isolates within Europe. And I'd say the fact that the Basques kept their language and culture, while the Sardinians only switched to Indo-European during Roman times, kept them isolated from a variety of admixture events that effected their more mainstream Indo-European neighbors.

Richard,

Whatever KO1 was, he's not quite as extreme an outlier as Loschbour and La Brana compared to modern and Neolithic Europeans, so he's probably admixed.

Eduardo Pinto said...

@David


When I last wrote, I had in mind your ANE_K7 calculator and not Laz's.
I understand you perfectly and I'm sorry for the confusion.

However, based on the ANE_K7 calculator and the levels of WHG-UHG it presents for Iberians - inbetween 50% and 60% - I still hold my explanation as at least somewhat valid, for I'm sure that in a near future we will discover that your WHG-UHG cluster represents not only European HGs but also North African and ME ones.

Davidski said...

Yes, that's probably true.

I'd correlate my K7 WHG-UHG cluster with the West Eurasian node in this schematic from Laz et al.

https://lh5.googleusercontent.com/-uWKxJyb3LUQ/U52yzg4-56I/AAAAAAAAAnc/7_FBtIZBmh8/w450-h249-no/Ancient_human_genomes_suggest_three_ancestral_populations_Fig2_small.png

But I don't know how close the correlation is.

ryukendo kendow said...

@ Davidski
Your point taken. I think the extremely high West Asian throughout the Aegean and Italy is one such separate phenomenon.

The point I am making, is that this isolation thing, when applied to the fringes of Europe, is the most imparsimonious and unlikely explanation of the data. We already know that 'Yamnaya had near east and Caucasus', and Yamnaya contributed 73% to Corded Ware, who were the pre-eminent source IE population in Europe. It follows that 'Corded Ware had 73% of the Near East/Caucasus of Yamnaya' and that this influence will be transmitted to all their descendant cultures. We also know that Caucasus/Near East influence is present throughout Europe except for non-IE speakers. Near East/Caucasus on the fringes off Europe seems pretty straightforward to me.

Were the slavs, and Balts especially, any less isolated from Cimmerians and Myceneans than Basques were? For Irish and Orcadian, who were not pure descendants of Halstatt, how much more West Asian must Halstatt be to produce Irish levels? 10%? And was all that derived from Mycenean/Hittite refugees and scythians in the forests of central Europe?

@ Chad
Razib also tweeted that Yamnaya is the most likely source of EHG/ANE influence in Europe, but mediated through Corded Ware.

I think the issue with WHG is either local survival, or expansion from some other locale with high WHG pops that had accultured themselves into the Bronze Age. BR1 was not a HG, but had high WHG and low EEF and a little bit of ANE, and also a nonlocal haplogroup. This is quite suggestive I think.

Two rather speculative observations: Razib tweeted that Reich was not sure if ANE in Western Europe derived from Corded Ware. Also, from PCA, if you add BR1 to Sardinians, you more or less get Basques.

Shaikorth said...

rk, proto-Indo-Europeans carrying a West Asian component would indeed explain many things shown by ADMIXTURE, for instance:


http://1.bp.blogspot.com/-LIug8kEPKW4/UFtC9XP-VsI/AAAAAAAAD1A/HTmsEscIGoI/s1600/MDLPwestasian.jpg

The difference between Northern Kargopol Russians (IE) and Karelians/Vepsians (not IE) in West Asian component when it appears @ K=7
http://biorxiv.org/content/biorxiv/suppl/2014/08/13/005850.DC2/005850-1.pdf

and here are no West Asian references so European I-Es including germanic, Italian and Northern Russian populations all start showing the same level of SC-Asian Balochi stuff instead @ K=13 while Sardinians have none and Basques almost none:
http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004393

The problem is that this is ADMIXTURE we're talking about, components created by modern populations don't necessarily correspond to ancient events so the stuff I linked isn't enough. The CW/Yamnaya paper will hopefully solve the "West Asian" issue and many others with more testing.

Davidski said...

Before I saw the results for BR1 in the K15, I would've agreed that probably all Yamnaya and Corded Ware groups carried some of that West Asian stuff, from contacts with late Neolithic West Asians via the North Caucasus and/or Balkans.

But considering that BR1 is from the Carpathian Basin of the early Bronze Age, and clearly not from the same population as the earlier Baden Culture sample CO1, then as things stand nothing is certain for me in this respect.

Early Yamnaya migrations affected the late Baden Culture, precisely where the Gamba et al. samples were taken. So if BR1 isn't somehow related to this phenomenon, then I'm a monkey. And BR1 has 0% West Asian in the K15. I suspect some will show up in BR2, but that's a late Bronze Age sample with Y-DNA J2, so I'll be shocked if it doesn't.

Chad Rohlfsen said...

David,
If CO1 is ploting on the loschbour side of Sardinians, he should be about 20% WHG. Sardinians are 17%.

barakobama said...

Kind of of subject. Using an age-estimation K01 comes out being ~5 years old.

http://www.fc.id.au/search/label/Genealogy

At 5 he wouldn't be out in the open getting food for his tribe, he would have been watched over by adults, and a tribe of farmers would have had to forcefully taken him from a hunter gatherer village, if his head was a war trophy. I guess there could be other reasons besides war why a farmer tribe would have the remains of a dead hunter gatherer.

Chad Rohlfsen said...

Ryu,
I think they're going to backtrack from their statement about Corded Ware being 73% Yamnaya. I think they will change their wording to, "it can be fit as 73%" Yamnaya, but it is not likely. He told me that it is not a good source for direct ancestry from the East, for Europe. They are having issues trying to figure that out. We could still have a Yamnaya source, but it will not be like Samara. They are too Near Eastern, from the sounds of it. If Northern Europeans were already 40-60%EEF, then they are too Near Eastern to be a great source of our ancestry. We could still be 50% Yamnaya, just likely from the Dnieper Don and Kemi Oba type. Not from a group around 50%+ EEF.

Davidski said...

Table S14.10 from Laz et al. is showing 14% WHG for Sardinians. So Baden girl CO1 probably has at least that.

She also probably has some ANE, which works too, if the earliest Yamnaya people in the Balkans were similar to BR1. That would also explain the ANE in Basques, minus the West Asian stuff.

Chad Rohlfsen said...

I think that CO1 is actually something like 77/20/3. That sounds about right, from the looks of his plot.

Chad Rohlfsen said...

Her plot. Excuse me.

Chad Rohlfsen said...

KO1, might be something like 10/87/3. He makes a straight like, down from Loschbour, while Stuttgart is about to the end of the graph, SW of Sardinians. A straight line down from Loschbour indicates an ANE shift. He should shift to the left of Loschbour, if he has no ANE, with EEF. You should check that on f3 stats.

Chad Rohlfsen said...

Sorry, a straight 'line' down from Loschbour.

Chad Rohlfsen said...

Even 10/84/6, is possible. I can do some measurements

Chad Rohlfsen said...

The plot with Loschbour, KO1, C01, together.

CO1 looks like 68/30/2, on that

K01 looks like 20/77/3

Just on rough measurements

Chad Rohlfsen said...

KO1 is slightly more ANE shifted than CO1, on that graph.

barakobama said...

Chad, do you have a measuring system for PCAs and locations for WHG, EEF-ENF, and ANE, so you can predict someone's WHG-EEF/ENF-ANE based on their position?

Davidski said...

I'll try and check KO1's ANE level with formal stats tomorrow.

Chad Rohlfsen said...

I don't have a measuring system, but I can play with it on another app I have. I don't think that BR1 is an unadmixed invader. He is almost 1000years into the first forays. I think that they are a mix of a CO1 like people, and another that is in the ballpark of 30/50/20. That makes more sense for a Western Yamnaya, or Dnieper Don. It all depends on how many hunters were still roaming the Carpathian Basin, during that time. Those first two numbers could swap places, and the ANE decrease.

Davidski said...

BR1 looks like the result of this...

http://imageshack.com/a/img909/3649/2T8HPd.png

Certainly not an unadmixed descendant though.

Source for the graphic:

https://www.academia.edu/3535020/Two_IE_phylogenies_three_PIE_migrations_and_four_kinds_of_steppe_pastoralism

Chad Rohlfsen said...

Yeah, I kind of favor R1b, being more dominant in Kemi Oba, and R1a more dominant in Dnieper Don.
Even today, those two are kind of split along those two lines. L23 is pretty common along that route. Archaeologically too, they say the German Beakers that migrated to the SE, ran into similar physical types, unlike in movements to the West. Kemi Oba is supposed to be more Near Eastern like, than Dnieper Don. At least on that crazy cranio-metric stuff.

Chad Rohlfsen said...

Plus, the Dinaric and British I2a's MRCA is 6kya.

Davidski said...

This paper discusses the cultures and their burial customs during the period in question in the Carpathian Basin, and mentions the Mako Culture.

https://www.academia.edu/978573/Mounds_and_Mountains_Burial_Rituals_in_Early_Bronze_Age_Transylvania

There's quite a bit there about kurgans and tumuli, but I don't have the time to read it properly now.

Chad Rohlfsen said...

Mention of a Corded Beaker, 3000BCE+-. Not a surprise, Khvalynsk had them too!!

Chad Rohlfsen said...

Antropomorphic stelae, like Kemi Oba...

Chad Rohlfsen said...

Balkan / Aegean stuff coming in around 2100BCE, could be part of that J2.

Chad Rohlfsen said...

Stone-lined cysts, with stelae.. clearly Kemi Oba.

Thank you, David!

The Corded Beakers, serious Maykop influence with daggers. It makes sense. Hopefully, it's causation and not just correlation.

Chad Rohlfsen said...

Didn't these stelae end up in Kurdistan around 2100BCE?

Chad Rohlfsen said...

"Khvalinsk evidences the further development of the kurgan. It began in the Samara with individual graves or small groups sometimes under stone. In the Khvalinsk culture one finds group graves, which can only be communal on some basis, whether familial or local or both is not clear. With the advent of DNA testing, perhaps someday it will be.

Although there are disparities in the wealth of the grave goods, there seems to be no special marker for the chief. This deficit does not exclude the possibility of a chief. In the later kurgans, one finds that the kurgan is exclusively reserved for a chief and his retinue., with ordinary people excluded.

This development suggests a growing disparity of wealth, which in turn implies a growth in the wealth of the whole community and an increase in population. The explosion of the kurgan culture out of its western steppe homeland must be associated with an expansion of population. The causes of this success and expansion remain obscure.

We do know that metal was available both in the Caucasus and in the southern Urals. The Khvalynsk graves included metal rings and spiral metal rings. However, there is no indication of any use beyond ornamental. The quality of stone weapons and implements reaches a high point. The Krivoluchie grave, which Gimbutas viewed as that of a chief, contained a long flint dagger and tanged arrowheads, all carefully retouched on both faces. In addition there is a porphyry axe-head with lugs and a haft hole. These artifacts are of types that not too long after appeared in metal.

There is also plenty of evidence of personal jewelry: beads of shell, stone and animal teeth, bracelets of stone or bone, pendants of boar tusk."

Huge match with these graves, plus that Kemi Oba, Mikhailovka twist.

Helgenes50 said...

A New hungarian neolithic is available
F999932

Davidski said...

Indeed, NE6 from Middle Neolithic LBK.

K15

North_Sea 0
Atlantic 22.5
Baltic 0
Eastern_Euro 0
West_Med 52.55
West_Asian 0
East_Med 20.16
Red_Sea 4.78
South_Asian 0
Southeast_Asian 0
Siberian 0
Amerindian 0
Oceanian 0
Northeast_African 0
Sub-Saharan 0

K13

North_Atlantic 11.44
Baltic 0
West_Med 58.44
West_Asian 0
East_Med 27.52
Red_Sea 2.61
South_Asian 0
East_Asian 0
Siberian 0
Amerindian 0
Oceanian 0
Northeast_African 0
Sub-Saharan 0

Helgenes50 said...

For the Neolithics, the results are really homo..geneous, and it is not just a way of speaking !

Chad Rohlfsen said...

Whoa! David, you have to run this one!!!

EEF 100.9005733
WHG -2.418198446
ANE 1.517625126

1 95.7% Sardinian + 4.3% Samaritan @ 12.24
2 95.9% Sardinian + 4.1% Lebanese_Christian @ 12.24
3 97.6% Sardinian + 2.4% Yemenite_Jewish @ 12.31


ANE -
ASE -
WHG-UHG 49.57%
East_Eurasian -
West_African -
East_African -
ENF 50.43%


Mixed results here. The calculator had them more extreme than Stuttgart. The date is so late, they are probably mixed a little.

Chad Rohlfsen said...

Not really, unless you compare it to Europeans now. NE7 looked like it might be more WHG than Sardinians. This one looks a little under.

Davidski said...

That's not bad, and it's probably a strong hint about things to come.

Earlier samples from the southern Balkans might look in large part Samaritan, minus any ANE of course.

Chad Rohlfsen said...

David,
Is it possible to throw Oetzi, BR1, and Gok4, on that plot as well? Or, if you want to stick to the Hungarians, throwing on NE7 and BR1 can help visualize the changes. Thanks!

Chad Rohlfsen said...

NE6, looks like they'll be 5-10% WHG. I think NE7 will be around 20%. NE4 looks more WHG than this one too. NE2,3,4, and kind of 6, are ANE shifted compared to KO2. You should do a plot with NE2.

David,
What do you think about revisiting the Gok farmers for ANE, since we have Stuttgart to plot them with now?

Chad Rohlfsen said...

I don't like their plot. It's hard to tell which way is up and which way is down. I'm not sure if NE2 or NE6 is more shifted.

Chad Rohlfsen said...

I think that it's more WHG than Stuttgart. Stuttgart could be modeled as 25% Tunisian Jew or Samaritan.

Chad Rohlfsen said...

David,
I know that you're busy with everything, but visiting the Gok farmers again, now that we have Loschbour and Stuttgart to plot next to them, could show something pretty interesting. If I remember correctly, Gok2 was between Sardinians and the Basque. She could be 5%ANE.

ryukendo kendow said...

@ Chad
I think what Reich was trying to say was that Yamnaya did not contribute directly, but only indirectly through Corded Ware. After all, they said that corded ware is most similar to north central Europeans today.

Could you do some new math on what you think are the ratios of Kemi Oba.and how they interact with what was preexisting in Europe to produce modern-looking europeans?

@ Davidski
BR1 contains an WHG - ANE mix, but of the wrong kind. He is not eastern European enough to account for the richness of that component in east europeans today. Or the east Europeanness of any population in Europe, for that matter.

If BR1 was a typical IE, and I find this highly doubtful, there must still be a huge wave of ANE and EEF-rich individuals later who introduced east euro and West Asian to Europe, and who played the greater role in driving up the East Euro percentage of East Europeans and others.

Chad Rohlfsen said...

I think that Gok7 was even more extreme than her.

Chad Rohlfsen said...

Ryu, his words that he thinks it's something related to it, but not like it. So a more WHG like Indo-European. People that mixed with WHG on the Western Steppes.

David,
Sorry, I cant remember who was more extreme. If it was Gok4 or Gok7. Plotting all three, with Stuttgart and Loschbour, could be an eye opener.

barakobama said...

It appears NE6 is a tiny winy bit more basal than Stuttgart. There's formal ways to find out who's more basal.

Chad, is the studying you do in admixtures saved somewhere in a way you can post? After looking at K15 today I realized it can reveal ALOT about population history.

Knowing the distribution of a component means almost nothing, it's all about statistics. Admixture results are a jumble of random numbers, but those numbers have patterns and reasons that can reveal alot!!! The only obstacle is how to find those patterns and reasons. If you defeat those obstacles you'll know exactly why everyone scores what they do, and every genetic layer and have a good idea in what order they came.

In my opinion good quality admixtures for west Eurasians like K13 and K15 are the result of several things.

1. BB-WHG-ANE-SS-EA.

2. Regional versions of BB-WHG-ANE-SS-EA. Baltic, N Sea, Atlantic, are all major components that express WHG, but are mostly determined by regional ancestry(Diff types of WHG?).

3.*Patterns-packages*: There's patterns-packages region by region. I've found a way to very accurately predict the North Sea score of a west Euro by knowing his West Med or Atlantic score. Because there's a west European package-pattern where those components are very intertwined.

Knowing how components work together(higher N sea means lower W Med) in region by region can help discover what percentage of a regionally mixed population's(eg, Austrians) Baltic, N Sea, E Euro is from NE Euros, NE Euros, SE Euros. And in the end you'll get an idea how much NW vs NE vs SE ancestry Austrians or whoever have.

4.*Isolation-Drift-Uniqueness*: Some populations like Basque are on their on and don't fall under any regional patterns-packages. K13 and K15 aren't very fit for them(like with many ancient genomes), so they get strange results. NW African's results in admixtures not designed for them can largely be explained by this.

Ancestry from an ancient population that's not fit for K13 and K15 can cause population's results not to fall under any regional patterns.

The Hinxton's barely fall under NW Euro patterns, and BR1 doesn't fall under any modern patterns(I don't think K13 and K15 are fit for him).

South Asian's results in ANE K7 is a great example of this. Their south-Asian specfic ancestry isn't expressed wasn't expressed in any of the components. People throughout west Eurasia scoring in "Jewish" components is another example.

barakobama said...

Davidski, BR1 didn't score in East Med even though he had Stuttgart-like ancestors. So, just because he had some eastern Yamna-like ancestry but no west Asian, doesn't mean Yamna won't score in west Asian. K13 and K15 overall aren't fit for him. He doesn't fit in any region of Europe today, he scored in NW and NE components to express his WHG, kind of like Loschbour.

Davidski said...

rk,

I never said BR1 was a typical IE. I do believe that's a straw man.

What I said was that BR1 was the result of the first Yamnaya migrants into the Carpathian Basin mixing with the Baden Culture people.

These first incursions seemed to have lacked the West Asian component, which by the looks of things, only appeared in the Balkans during the late Bronze Age.

I very much doubt that we can put all of the post-Neolithic changes in Europe down to a single Proto-Indo-European wave. It's more likely there were many waves, big and small, and they weren't all genetically identical. BR1 and IR1 hint at this very strongly.

ryukendo kendow said...

What he said was it 'was not a realistic direct source population'. Not that it was not a source pop. If you had asked him about corded ware, the answer will no doubt be different. If you asked him if it were 'related' to Yamnaya, ditto.

If I remember correctly, you once explicitly rejected the idea of high WHG IEs, because you could not get the math to work. So you proposed mesoLithic survival. What is different now that you are postulating a high WHG Kemi Oba?

@ Chad @ Davidski
Note that the ANE - WHG affinities of BR1 are with mesolithic components that are already present, not with East Euro. So the modern pops in the area could not have been IE-ized by this pop only. Rather, if he were indeed IE, West Europeans could have been.

Davidski said...

Barak,

BR1 looks like a mix of Baden, KO1 and something from the east.

But it's really not very Caucasus/West Asian-like in any of the tests I ran. This is not part of the package.

Davidski said...

rk,

You're not arguing against what I said, but apparently with what you assumed I said.

ryukendo kendow said...

I think it is possible that he was ie, just that this doesn't solve any of our problems. Because Europeans today differ from a KO1-CO1 mix by having east euro and West Asian, in quite a large fraction combined, and BR1 has none of either even though he has ANE, either he was not a significant contributor to the process in the east but could be in the West (east euro and West Asian are maxed in the East but not in the west), or he was not IE.

barakobama said...

"But it's really not very Caucasus/West Asian-like in any of the tests I ran. This is not part of the package."

What types of tests did you run? Is BR1 more west Asian/Caucasus-like than Lithuanians or Irish who score in west Asian components? Can your tests go beyond ENF-WHG-ANE, and break down to regions?

Chad Rohlfsen said...

Barak,
I don't get hung up on the labels anymore. They look like they're just mushed together as representative of where you fall. For instance, if your ANE is higher than your WHG, it tosses you west Asian. If the farmers that went through the Caucasus are like the ones in Europe, but contribute over 50% of the genes, and the ANE is comparable or more than the ANE, you'll get west Asian and maybe east or west med, depending on how much of a drop there is. As long as someone doesn't have a bunch of non European genes, it's easy to figure them out, by the plot.

It seems basque don't score west Asian, because their WHG to ANE ratio is too high. British only need a couple percent of west Asian, to make their ratio. The labels are misleading. Remember the ibd sharing had more relation to ir1, for basque and Sardinians, than Brits. The case of ir1, looks like he does have a bit of East Asian, as he drifts out just past other Balkan people who do. He's a bit of an outlier because of that.

Chad Rohlfsen said...

If ANE is comparable or more than WHG, you get west Asian as a component in a good chunk.

Davidski said...

There's nothing wrong with BR1's K15 results. If they were misleading then the oracle results wouldn't make any sense, but they obviously do, and it can't be a coincidence.

Anyway, here are the plots for NE6, Stuttgart and Oetzi. Keep in mind that the quality of the genotypes also matters, and Oetzi here is a bit lacking in this respect.

I can't plot them all together, but you get the idea; NE6 is obviously ANE free.

https://drive.google.com/file/d/0B9o3EYTdM8lQNFJYMmtVaUVfN2M/view?usp=sharing

https://drive.google.com/file/d/0B9o3EYTdM8lQNjNYVl9xUEVtUE0/view?usp=sharing

https://drive.google.com/file/d/0B9o3EYTdM8lQUWhXQXcxUU9zNGM/view?usp=sharing

Shaikorth said...

BR1 has extremely low East Euro and has a mean coverage of 0.81. In the PCA of projections in the article he could just be a mix of EEF and SHG (Ir8) types. But the CW and Yamnaya papers should soon enough reveal if he has anything to do with PIE populations.

Davidski said...

I don't see what the problem is?

We've had archeologists writing for decades about the late Baden Culture being influenced by migrants from Eastern Europe, and now we have a genome from the immediate post-Baden Culture period that looks partly Eastern European.

Unless there were two parallel migrations into the Baden Culture region, both from Eastern Europe, but one Indo-European and the other not, then it's very clear what's going on here.

barakobama said...

Chad,
"I don't get hung up on the labels anymore."

There's obvious regional representatives of ENF-WHG-ANE, that's why Czechs and English score differently. Regional representatives and patterns-packages are the main drives that cause people to score in what they do, uniqueness-randomness and overall ENF-WHG-ANE, are almost always the minor reasons.

The labels are very leading in my opinion. For the most case modern pops share the same packages and regional variation, Basqueism is pretty rare. Therefore if you unlock those patterns you can get an accurate what a samples regional makeup is. I understand there is some randomness, like near easterns and south Asians scoring in N European components.

Europeans scoring in west Asian components is probably a mixture of randomness and patterns-packages. I doubt it's only because of left-over ANE because why do Motala12 and MA1 lack it? Don't forget Iberians and SW French have around as much ANE as Basque but score as much in west Asian as NW Europeans.

Chad, I think there's alot of good info in K13 and K15, which we have to dig for to find. I think you may be underestimating it. For example after just a few hours of looking for patterns in K15, I changed my initial opinion that Baltic was non-existent in Sardinian-like Neolithic west Europeans and was introduced by Indo Europeans, because Iberians-SW French's Baltic wasn't all in the same pattern-package as NW European Baltic. Then I saw C01 scored in Baltic.

barakobama said...

Everyone is so focused on autosomal DNA that it seems they've forgotten about parental markers. There are plenty of Yamna mtDNA samples, why not compare them to the 100s of mtDNA samples from early central European farmers and modern Caucasus-near easterns? I remember Yamna belonged to many European-specif near eastern clades and was split at ~50/50 between typical eastern hg mtDNA and near eastern mtDNA.

Chad Rohlfsen said...

Barak,
SW French are almost 10% less WHG than Basques. So, they need a West Asian representation.

Our Neolithic samples are mostly West Med, which has a negating effect on WHG and ANE. They need North Atlantic, to pull the ANE and WHG up over 0. Then the East Med drops the extra WHG picked up in the Atlantic component. It's not perfect, but get's them very close to where they should be.

Chad Rohlfsen said...

Baltic is too high in WHG and ANE. There isn't anything that negates ANE enough to have Baltic show up in our farmers.

barakobama said...

CO1 had Baltic, Basque have Baltic, Sardinians have Baltic. Everyone in Europe scores a little Baltic. Remember all the hunters including western ones scored in Baltic, so excess Western hunter in European farmers, may be giving them Baltic. North Sea though is obviously the destination extra and very pure WHG in farmers goes to first and most often though.

Also, extreme-Mediterranean scores for EEF is mostly a result of the regional factor I mentioned, because why don't they score in near eastern components?

I think we should trade ideas, strategies about admixtures, and work together. Because you think of things I would never think of, have different strategies, etc. It's better to have multiple brains and workers instead of one. Plus were both have the same goal.

I don't have much so far(it's been one day) but I can give you files and filled-out maps I have saved. Do you know of anything online that can fill out maps with the distribution of a component, pattern, etc?

Chad Rohlfsen said...

Farmers have to show East Med, to negate WHG from Atlantic. Just as modern Near Easterners need it to negate all of their WHG/UHG. The labels aren't to be taken literally, but can show affinity. Remember components are all modern, ancients are going to look screwy.

Yeah, you can e-mail me. chadrohlfsen@hotmail.com

Let me know if you send something. Basically everyone that I don't email first, get's spammed.

Chad Rohlfsen said...

Personally, I think that plots can be better in some instances, for inferring EEF/WHG/ANE.

When it comes to Czechs and English, there is a couple things to remember. If people have basically the same EEF, but one has a tad less WHG and a bit more ANE, they are going to pull to the SE. WHG and ANE are equidistant from Basal Eurasian. Since Stuttgart and therefore Basal go to the SW, ANE/Mal'ta have to shift to the SE, in the direction of the Mari, but well past.

Chad Rohlfsen said...

With a plot big enough, I could find the basal and WHG/UHG percentages of a near eastern population. Preferably one with almost no ena, or ssa, as a start.

Chad Rohlfsen said...

All it would take is loschbour, ma1, and Stuttgart, with European and west Asian pops

barakobama said...

Chad I just sent you the email. Sorry if the maps are hard to read.

Here are the links from it anyways.

https://docs.google.com/spreadsheets/d/1kbEaP9EQzOHdu3-Mfqmrnso2jmquC8sD3FC4F3qR5d8/edit?usp=sharing

https://docs.google.com/spreadsheets/d/1EPs6gfWlTHNqyCZgTaw6wbm7_q4DbNld3J9csRiQA2k/edit?usp=sharing

https://docs.google.com/document/d/1fLwwijkqH_Xyeb0mlIf-bFfpZAFsLZz5iUktqfS1ynQ/edit?usp=sharing

It's very basic math but I think it can be useful. These are just my personal notes from one day, I think I might be on to something or I will be eventually.

ryukendo kendow said...

@ Chad
Appreciate the great work you're doing.

On another note, I highly doubt that components in ADMIXTURE can negate each other in any sense, however.

The West Asian in other's runs, incl Laz's, typically have no ANE contribution to speak of, and thus cannot represent ANE 'left over' in Europe.

How are you controlling for the fact that pure WHG individuals score in very different places in a single plot?

@ Davidski
Its far from clear to me at least. All indications are so far that IE Europeans differ by having sizeable amounts of East European and West Asian, with ANE segregating into both in your runs and ANE into East Euro and Basal into West Asian in other's runs.

However the WHG-ANE and Basal components in BR1 have neither. So its simply not clear that he or someone who kurganized him was responsible for the change. The only way he could still be IE is if the people who kurganized him Kurganized Western Europe, shifted things in a Motala-like direction and produced something like an extreme 'NorthWestern' Hinxton, but that doesn't explain anything as it means that later waves of IE are needed to kurganize everyone again anyway, including the 1) those who did the kurganizing for BR1, whoever their closest desc were and 2) Hungarians themselves.

Last of all this raises the issue of the model for the spread of IE. Of course, IE spread in multiple waves, but the people were once a single dialect community, and that is not so large that the people in different parts have sub-continental differences in their autosomes. This might change over time of course.

For these reasons I think BR1 is part of a separate phenomenon, of which there were many at this time.

@ Chad
Could you provide a WHG estimate for Uyghurs, Uzbeks or Kazakhs from their K13 numbers?

Uyghurs especially, because they are part tocharian, which is centum; and Greg Cochran thinks that centum IEs might have WHG while Satem ones don't. If that is the case it might fit David's scenario of early movements having IE.

ryukendo kendow said...

Sorry, having WHG.

Chad Rohlfsen said...

Ryu,
These components do negate each other. Here again, are some examples.

Atlantic
EEF 36.09902375
WHG 46.76502641
ANE 17.13594984

Baltic
EEF 19.65489078
WHG 57.48490214
ANE 22.86020708

West Med
EEF 104.3728415
WHG -2.811381618
ANE -1.561459894

West Asian
EEF 88.75184039
WHG -2.440100982
ANE 13.6882606

East Med
EEF 120.4910719
WHG -21.62230786
ANE 1.131235957

Red Sea
EEF 113.5571898
WHG -16.85837478
ANE 3.301184967

So, you see why we get farmers having Atlantic, to score WHG and ANE in the positive, then East Med and Red Sea to then reduce both back towards zero.

I can work on some figures later. I would need something huge, including East Asians, to figure out anyone with more than a couple percent of ENA. I feel better focusing on West Eurasians for now.



Chad Rohlfsen said...

Barak,
Excellent maps and work. I would expect a pattern for people that share that much history. Where you may see differences in going to SW French, is mostly in the Med and West Asian area. There appears to be more of a WHG holdout, or not a lot of admixture after the Bronze Age. Although, seeing IR1 sharing decent snps with the Basque and Sardinians, it makes me wonder about the effect of Greek colonization, for SE Iberia and Southern France. That's the only thing I can think of, as far as them sharing more IR1 ancestry than Brits. It must be Greek driven for some. Britain may just not have received much input from Indo-Iranians, in any kind of way.

barakobama said...

Who's the guy that created the K13 EEF-WHG-ANE calculator? We should ask him to do the same for K15(hopefully it'll be more accurate), and how he did it. The EEF, WHG, ANE score of every component I think is based on score of solely European populations who got estimated for EEF-WHG-ANE in Laz.

North Atlantic obviously means different things for different populations. For Iberians it's very EEF-like for Nw Europeans it's very WHG-like. It's made more clear in K15 with the split into North Sea and Atlantic.

We have to come to peace with the fact there is no method out there that can accurately predict EEF-WHG-ANE. The K13 calculator isn't perfect, and Laz wasn't perfect. ANE K7 isn't perfect and PCAs aren't always perfect for doing this.

We can only get general ideas and shouldn't treat any of this as concrete or fact.

Chad Rohlfsen said...

Barak,
West Germans are more ANE and WHG than the French. They should then score a little more in either Baltic or North Sea, plus West Asian. French should be higher in Atlantic and West Med.

ryukendo kendow said...

What I meant was, since there are so many different ways to get the same percentage, why does ADMIXTURE only choose one? Why don't neolithics become dominated by red sea + Baltic?

The West Asian no ANE thing is from the observation that Mal'ta generally score 0% in West Asian in most ADMIX runs. Mal'ta does score in Indus-centered and E.Euro ones in other runs though.

For Uyghurs, I mean, use ADMIXTURE k15 components to figure out. Since we can get rid of the east Asian half of C. Asians simply by removing their scoring in those and compare the rest.

Chad Rohlfsen said...

If West Med, was made a little more negative, say -4.5% ANE, it would be almost perfect. But, then other components would have to be changed, to compensate.

ryukendo kendow said...

Sorry I meant k13.

Chad Rohlfsen said...

I think that PCA plots are the easiest way. You just have to have an idea of a population's average score. It won't be perfect, but you can get very close.

Chad Rohlfsen said...

Ryu,
Farmers cant be Baltic and Red Sea, because of all of the WHG and ANE in Baltic. Red Sea will not reduce the ANE as much as the rate of ANE to WHG in Baltic.

Chad Rohlfsen said...

Red Sea is in the positive for ANE. Only West Med is in the negative. It's the most important component for every Neolithic sample.

ryukendo kendow said...

@ Chad
Huh?
I'll rephrase: If Admixture were a simultaneous equation solver, which is what you're describing, an equation with 13 variables and 3 knowns has by definition an infinite number of solutions.
So, that ADMIXTURE picks one so readily cannot be due to ratios only.

barakobama said...

"Excellent maps and work. I would expect a pattern for people that share that much history."

The pattern doesn't apply anywhere else in Europe, except somewhat in South Dutch. North Sea people score high in Atlantic and North Sea, so they have somewhat of their own pattern.

What I want to eventually do is create a proxy score(very speculative) for what changed west Europeans after the Neolithic. It might not work because we're talking about ancient populations who aren't fit for components based on modern people. I expect something like Hinxton 2 and 3, to at least be apart of it.

I can't figure any common patterns between the the Hinxtons and modern pops, expect somewhat with North Sea people. Their results are very strange, and it varies among different Britons and Anglo-Saxons. I think this is because of the uniqueness-randomness factor, and should be taken lightly.

I suspect North Dutch are a mixture of the W Germ-French-SW French pattern and the North Sea pattern, so their Atlantic doesn't change much, but their North Sea goes way up.

That formula I created might turn out to be useless. I wish I could get exact numbers, but the randomness-factor is to strong, and I'm not very good at math.



Chad Rohlfsen said...

None of the components can be portrayed as IE. It all depends on population structure, prior to IE arrival. Someone could have basically zero West Asian, and have a lot of IE input, or have a decent amount of East Euro, and have hardly any IE input.

Chad Rohlfsen said...

We need to know what the populations were like prior to IE, and who exactly invaded Europe. The Samara Valley isn't a good fit, and represents only a small place in space and time, prior to migrations.

barakobama said...

"Farmers cant be Baltic and Red Sea, because of all of the WHG and ANE in Baltic. Red Sea will not reduce the ANE as much as the rate of ANE to WHG in Baltic."

Are you basing this on the K13 EEF-WHG-ANE calculator? It might be false. Besides we already have farmers scoring in both red sea and Baltic.

"Since we can get rid of the east Asian half of C. Asians simply by removing their scoring in those and compare the rest."

In my experience this doesn't necessarily work, because of the randomness factor. IF we took out Sami's east Asian admixture, they would turn out like a Mesolithic European with almost no near eastern ancestry. When in reality their non-east Asian ancestry is probably similar to NE Europeans, so they has a big chunk of EEF(over 30%).

I tried doing this with my uncle's results to see what his grandmother's results would be. I came out with a bunch of negative scores, and it was just really screwed up overall. I tried it with central Asians to see what their non-east Asian ancestry is, and put in the K13 calculator. I think it came out like 13% ANE, 20% something WHG, and over 60% EEF. It didn't look good.

ryukendo kendow said...

@ Barak
Oh, looks like you have already done it. Thanks! I thought it would be kinda screwed up, but just wanted a ballpark estimate. If they turrned out with ridiculous WHG like BR1 then something significant is going on.

@ Chad
Huh?? You have to understand exactly what ADMIXTURE is doing before saying anything like that.

Several articles ago somebody already pointed out that not even the ANE K-7 was producing consistent results for WHG in Europeans. What makes ADMIXTURE so powerful sudddenly in K=13, that even combinations of the three can be figured out? ADMIXTURE does not have the capacity to do that.

What admixture can do is tell us which autosomal affinity exists in which population where. The only thing we know right now is that an affinity that peaks in East Euros and West Asians did not exist in Europe prior to IE.

In terms of ADMIXTURE at least, what came before does not matter, because we know already that whatever came before it was not these two.

Chad Rohlfsen said...

Farmers with Baltic have WHG over Stuttgart.

barakobama said...

'Although, seeing IR1 sharing decent snps with the Basque and Sardinians, it makes me wonder about the effect of Greek colonization, for SE Iberia and Southern France'

I suspect there's east Mediterranean ancestry throughout Europe. Italy and the Balkans show strong signals. Iberia obviously has some to. I Hope to find a way to create a speculative proxy of European's recent east Mediterranean ancestors and see if it closely matches any modern near easterns. Parental markers can probably give clues.

There a big break off between Spain and SW France, in terms of that package I mentioned. Basque are somewhat a continuum of the W German-French-SW French trend though.

I believe east Med-admixture may have caused Iberia to break off from this pattern. Iberians may have been more SW French and Basque-like in the bronze and Iron ages.

Eduardo Pinto said...

@Barak

IMO, The difference between East_Med and West_Med is that the former is an unadulterated form of basal eurasian whereas the latter comprehends some UHG influence.
The same could be said about the Atlantic cluster but in a lesser degree.
So we can safely assume that East_Med > West_Med > Atlantic represents a cline of basal eurasian over WHG/UHG influence.

Davidski said...

IR1 shares a lot of drift with Basques and Sardinians because Neolithic farmers who populated the Balkans also contributed ancestry to Basques and Sardinians. And IR1 is partly of Neolithic Balkan origin, just like CO1 and BR1. All three of these samples are related, it's just that BR1 and IR1 carry unusual, non-local admixtures compared to CO1.

ryukendo kendow said...

@ Davidski
Agree.
One thing that is weird to me however, is why these populations, who are putatively IE, do not share more with IE pops in Europe than non IE pops. After all, if these samples are IE, then Europeans in general are Neolithic + IR1/BR1 mixes, so shouldn't they all rank higher than Basques and Sardinians?

Are there issues of IBD length?

Davidski said...

Lithuanians, Basques and Sardinians have relatively less complex ancestry than other Europeans, with high levels of the basal components that make up present-day Europeans. That's why they act like magnets in the shared drift tests for certain groups: Lithuanians for Northern European/hunter-gatherer genomes, Sardinians for Southern European/Neolithic farmer genomes, and Basques for those that are mostly a mixture of the two.

Chad Rohlfsen said...

Sardians and basque were in the cardial group, not Danubian.

Chad Rohlfsen said...

Okay

Matt said...

Honestly, I think 2 dimensions and mixes of WHG-ANE-ENF points on them probably will works pretty well to describe the Eurogenes components (if that's what you wanted to do), after having a go at transforming the distances between Eurogenes components into PCA dimensions, then transform from these back into distances (there's a function in the PAST software Davidski's linked to before that seems useful for this, if I'm using it right).

Where there isn't a close fit between the first 2 dimensions and table of component FST divergences mainly relates to distances between the Atlantic, North Sea, Baltic components, where the components have higher FST divergences than would be predicted based on the PC (e.g. take North_Sea and Atlantic, and they get compressed quite close on the first 2 dimensions of PCA but show a direct distance from one another that's actually about 1/2 as high as each have from West Med).

But as these components tend to co-occur in populations anyway, and I'm not sure there were ever any Atlantic or North_Sea people running around, I'm not sure this has much significance in terms of modern day populations.

Grey said...

@rk

"Last of all this raises the issue of the model for the spread of IE. Of course, IE spread in multiple waves, but the people were once a single dialect community"

Does that necessarily follow?

There are numerous recorded instances from later history of tribes on or near the steppes being displaced by pressure from the interior and in many of those cases the displaced tribe makes an agreement with a neighbor on the opposite side from the pressure for safe passage through that neighbor's territory.

If Yamnaya is the epicentre of the IE expansion then it won't have achieved that status over night. It would have gradually developed an advantage over its neighbors over time and during that period when it was gradually imposing itself on its nearest neighbors some of those neighbors might have simply moved away.

This seems far more likely to me than a Yamnaya expansion out of the blue.

If this was the case then the first "IE" wave might not be IE. Although if this was the case then they would have originally been adjacent so they might have some similarities but maybe not the same language or the full package.

The IE wave came second.

In which case in the Hungarian example it would be original pop. x + non-IE wave y1 + IE wave y2 = final result z

Grey said...

"and I'm not sure there were ever any Atlantic or North_Sea people running around"

If clines exist along the various routes taken then as well as east-west and north-south i'd guess a coastal cline would go something like

Baltic -> North Sea -> Atlantic -> West Med -> East Med

ryukendo kendow said...

@ Grey
I think thats perfectly plausible. After all the first putatively IE cultures had weapons of stone. So there's been quite a bit of cultural variability there, prob with autosomal variability to match.

I think that there must be however a stable set of autosomal similarities. While neolithics in Europe had megalithics, danubian, cardial, all had west med at least, even though they might have different secondaries, e.g. Megalithics was Atlantic, like you said. They all shared some west med connection, which means that we can triangulate back to this pop.

I find it doubtful that some IEs had no East Euro and West Asian, and others did massively, unless one wants to switch primaries and secondaries and argue that the primary source pop for IE was baltic/Atlantic/West Med dominated, and that the ANE in BR1 was from this IE pop, and the Yamnaya were kurganized by this IE pop. This scenario just doesn't fit in any way.

Grey said...

"I find it doubtful that some IEs had no East Euro and West Asian, and others did massively"

I don't think they're IE. I think the source region is the intersection between three distinct ecozones: farming, forest and steppe and the three populations associated with those ecozones: west asian (cucuteni imo), WHG and EHG (aka ANE aka PIE).

So this presumed mostly WHG pop. are adjacent to PIE (with maybe some cultural similarities to PIE hence the confusion) as PIE are in the process of turning into IE and the WHG pop. get displaced by them.

If correct your problem

"However the WHG-ANE and Basal components in BR1 have neither. So its simply not clear that he or someone who kurganized him was responsible for the change. The only way he could still be IE is if the people who kurganized him Kurganized Western Europe, shifted things in a Motala-like direction and produced something like an extreme 'NorthWestern' Hinxton, but that doesn't explain anything as it means that later waves of IE are needed to kurganize everyone again anyway, including the 1) those who did the kurganizing for BR1, whoever their closest desc were and 2) Hungarians themselves."

becomes x + y1 + y2 = z

where
x = base pop.
y1 = mystery pop.
y2 = yamnaya
z = hungarian

so

x (base pop.) + y1 (mystery pop.) = BR1

and

BR1 + y2 (Yamnaya) = z (Hungarian)

so it should be possible to figure out the components of the mystery pop. y1.

Chad Rohlfsen said...

David,
Felix has K8 from Bulgaria, uploaded.

Davidski said...

Yeah, I know. That's the supposedly contaminated one, and it does seem that way. It almost looks like one of the researchers typed himself or herself.

K15

North_Sea 26.31
Atlantic 42.04
Baltic 0
Eastern_Euro 0
West_Med 22.43
West_Asian 0
East_Med 0
Red_Sea 6.51
South_Asian 0
Southeast_Asian 0
Siberian 0
Amerindian 0
Oceanian 0.03
Northeast_African 0
Sub-Saharan 2.69

K13

North_Atlantic 62.26
Baltic 0
West_Med 26.3
West_Asian 0
East_Med 0
Red_Sea 7.1
South_Asian 0
East_Asian 0
Siberian 0
Amerindian 0
Oceanian 0.32
Northeast_African 0
Sub-Saharan 4.01

Chad Rohlfsen said...

EEF 60.92238694
WHG 28.03840265
ANE 11.03921042

Yeah, that is pretty similar to BR1. It doesn't look right.

Chad Rohlfsen said...

How is M4 looking?

Davidski said...

There's nothing I can do with that sample. It has too few SNPs.

It's late Bronze Age anyway, so it doesn't say much about the Single Grave Culture. We'll just have to wait for the Corded Ware genomes from the new Laz paper.

Chad Rohlfsen said...

Yeah, hard to say. Bronze was taken there by Beaker around 2300BCE, so it's pretty late.

Are you going to revisit the Gok farmers and hunters, now that we have Loschbour and Stuttgart? That would be very informative to the pre-Copper shift towards WHG and ANE.

Davidski said...

Ajvide58 is basically like Motala12, but with less ANE.

I'll look at Gokhem2 again when Felix uploads his file of that genome and it has more SNPs than the one I've got.

Chad Rohlfsen said...

He has Gok4,5,an 7. Those are pretty good too.

BTW BR2 is done!

Chad Rohlfsen said...

4,5, 'and' 7. Sorry.

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