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Friday, February 3, 2017

First look at Latvian and Ukrainian ancient genomes


Below are three plots featuring ancient genomes from the recent Jones et al. paper on the Neolithic transition in the East Baltic and Ukraine. The relevant data is available here, and compatible with my Days of High Adventure, Basal-rich K7 and Global 10 analyses, respectively.

See anything interesting? Feel free to share it in the comments. Please note, however, that I can't guarantee that the results will make perfect sense for all of these samples, most of which have mean genome-wide coverage of less than 1x.




Citation...

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

See also...

No game changer

201 comments:

1 – 200 of 201   Newer›   Newest»
Arza said...

Global 10
nMonte

Latvian
Unetice_EBA:I0047 66.7
Latvia_MN1:ZVEJ26 25.95
Latvia_MN2:ZVEJ31 7.35
distance%=0.477 / distance=0.00477


Lithuanian
Unetice_EBA:I0047 74
Latvia_MN1:ZVEJ26 21.25
Latvia_MN2:ZVEJ31 4.75
distance%=0.5302 / distance=0.005302


Belarusian
Unetice_EBA:I0047 86.7
Latvia_MN1:ZVEJ26 13.3
Latvia_MN2:ZVEJ31 0
distance%=0.4008 / distance=0.004008


Polish
Unetice_EBA:I0047 88.1
Latvia_MN1:ZVEJ26 11.9
Latvia_MN2:ZVEJ31 0
distance%=0.4986 / distance=0.004986


Finnish
Unetice_EBA:I0047 53.65
Saami 30.85
Latvia_MN1:ZVEJ26 15.5
Latvia_MN2:ZVEJ31 0
distance%=0.2791 / distance=0.002791

Artists impression:
https://4.bp.blogspot.com/-L0Y3oyCvP10/WJS5NWk7OMI/AAAAAAAAAGU/iCLvbEXg9cwtTokT21i-i-9ansq2ve9MQCLcB/s1600/clinemap.jpg

Alberto said...

Great, thanks!

I've been running the samples with the Global 10 data, with all the combinations, weighted and unweighted, and here is the short version (unweighted, since it was almost identical to weighted and anyone can reproduce it):

https://docs.google.com/spreadsheets/d/12LI5EdWNjpzpxxaSeU_GDj0nTfApnMz9iZJcytmjSWs/edit?usp=sharing

- Latvian HGs between SHG and WHG, closer to SHG. The third one already gets 4-5% CHG admixture (Motala it self usually get a big of CHG too).

- Latvia_MN1 is close to WHG but with some 15% CHG admixture (in a weighted run it got 2% Paniya, probably that's why in the paper it also got that stat with Papuan - noise?)

- Latvia_MN2 is almost an EHG, slightly shifted towards SHG.

- Latvia_LN1 is a very peculiar Corded Ware sample. It has no European_MN admixture (or Anatolian farmer), and instead it's a Yamnaya-like version with SHG instead of EHG.

- Ukraine_HG would be close to SHG, but slightly shifted towards EHG. But it also has some 11-12% CHG admixture (this is 9.000 BC, right?)

- Ukraine_N1 is quite similar, slightly more EHG, slightly less CHG.

Shaikorth said...

D-stats don't show CHG in Ukraine or Latvia_MN1. What happens if you add MA-1 and AG3 as sources?

Alberto said...

@Shaikorth

Nothing happens with MA1 and AG3. None of the samples get any of it (unless I run without EHG). I'll test now with just Loschbour and AG3, but I don't think that will affect the CHG figures.

Here is without Motala, which actually makes CHG go up a bit (as expected).

https://docs.google.com/spreadsheets/d/1VrvkO7plCfFdKLX2gHAjexsyG_5fViLjY8sRjKNie80/edit?usp=sharing

Alberto said...

Yes, no change:

https://docs.google.com/spreadsheets/d/1O6KDy-QOdd6JED_5mZ3i-HRx3RcVFCyBCVNNAA_HQ1Y/edit?usp=sharing

(These last 2 are with weighted values, for no particular reason. They're within 1-3% variation without weighting).

Shaikorth said...

That's kinda odd since the D-stat Mbuti Kotias Bichon UkraineHG/N is very much insignificant.

Maybe they're related to non-basal extra in Kotias?

Can you test with Kotias changed to Satsurblia or Iran_N, also including WHG, SHG, EHG and AG3?

Alberto said...

I just think that Kotias and Satsurblia never perform very well in D-stats, so it's difficult to detect a small amount of admixture from them.

Here is one of the long versions that I tested:

https://docs.google.com/spreadsheets/d/1ptEcrr84bBYpiugpS4tqmvsFpisCYbwEKJ9t0Qr0DmU/edit?usp=sharing

I think that a stat like D(Mbuti, Ust-Ishim)(Loschbour, Ukraine_HG1) will show that there is basal Eurasian admixture in Ukraine.

Romulus said...

@Shaikorth

"Maybe they're related to non-basal extra in Kotias?"

That's exactly what was already said about the Villabruna cluster in the Villabruna paper. The formation of Villabruna cluster brings increased affinity to east asians and near easterners represented by the non Basal-Eurasian part of CHG.

FrankN said...

Alberto - can you run MN2 with either Kennewick or Karitiana included as source pop?
From the paper: "Latvia_MN2 is placed toward EHG in PCA space and has several components in ADMIXTURE analysis that are found in Native Americans, Siberians, and hunter-gatherer samples from the Caucasus.".
In fact, as per their Table 2, the highest Z-score comes with D(Mbuti, Zapotec)(Latvia_HG,Latvia_MN2). D-stats with Kariatiana are almost as significant as with Karelia_HG.

EastPole said...

I have run Basal-rich K7 with new samples. Here is PCA:

http://s29.postimg.org/x7z0o6htj/pca12_Baltic_All.png

My preliminary observations:

Latvia_LN1 can be modeled as a mix of Ukrainian HGs an Caucasian HGs like Kotias (red arrows)

CWC can be modeled as Latvia_LN1 and EEF (blue arrows).

http://s29.postimg.org/m3x0zm307/pca12_Baltic_All2.png

This agrees with my hypothesis is that Latvia_LN1 comes from proto-Balto-Slavic R1a dominated Late Sredny Stog and not from R1b dominated late PIE Yamnaya.
Yamnaya most likely participated in the formation of Bell Beakers and Western European proto-languages from which Italic, Celtic and Germanic languages originated.
Sredny Stog was located west of Early Yamnaya and it is likely that more western HGs like Ukrainian HGs participated in its formation by mixing with migrating Caucasus groups.

CWC formed as a result of the migration of proto-Balto-Slavic Late Sredny Stog Dereivka culture north and west, mixing with EEF in Ukraine and Poland and HGs around Baltic. As a result of those migrations and mixing various early Slavic and early Baltic dialects originated.

http://s29.postimg.org/3k393atbr/image.png

Alberto said...

@FrankN

Sure, here it is:

Latvia_MN2:ZVEJ31
Karelia_HG:I0061 74.2 %
Motala_HG:I0017 24.4 %
Loschbour:Loschbour 1.4 %
Kotias:KK1 0 %
Karitiana 0 %
Kennewick:kennewick 0 %

Distance 0.003514

I think it's really difficult that they would take Native American input, since Amerindians have some 60% East Asian and 15,000+ years of their own drift. Probably the D-stats are similar to Karelia_HG because somehow both Amerindians and EHG have around 40% ANE, which is the part that drives the stat in both cases. Plus this sample has some Onge-like noise (?) which probably also contributes a bit to increase affinity to Karitiana.

With AG3 instead of Karelia_HG:

Latvia_MN2:ZVEJ31
Motala_HG:I0017 65.2 %
AfontovaGora3:I9050.damage 34.8 %
Loschbour:Loschbour 0 %
Kotias:KK1 0 %
Karitiana 0 %
Kennewick:kennewick 0 %

Distance 0.005175

Rob said...

I think these results strongly suggest there was a mass migration from the Caucasus (Majkop) to northern & western Europe

Chad Rohlfsen said...

NMonte creates phantom CHG. Those numbers aren't real. I've covered this ad nauseam. Why is anyone still using it? Get Admixtools and learn it.

Chad Rohlfsen said...

Negative. Beaker is low in CHG.

Chad Rohlfsen said...

They found no evidence of CHG in Ukraine. I'll have mine up and ready to test tonight.

Davidski said...

Nothing wrong with using nMonte with plausible reference samples. Whether CHG is plausible in this case is another question altogether.

I'm testing that now.

Rob said...

@ Chad
I think your comments are over reaching
Yes there minimal CHG with nMonte in Ukraine in either Neolithic or Mesolithic (10-15% at best). If true, it means it rose in later, in the Late Eneolithic (immediate pre-Yamnaya period)

Chad Rohlfsen said...

We'll see. I'll be testing them soon.

Alberto said...

Yes, there's nothing strange or implausible in Mesolithic Ukraine having admixture from the Caucasus. They tested in the paper for that reason. This are the stats:

Mbuti EHG WHG Ukraine_HG1 0.0237 1.417 15359
Mbuti CHG WHG Ukraine_HG1 0.0143 0.915 16477

By the low number of sites, probably only transversion, so the Z is low. But look at the values, they're quite significant. And now think that Ukraine_HG is about 45% EHG. Why wouldn't those stats show that it is also 10-15% CHG?

Test it and you'll see that's probably correct.

Matt said...

Re: the Days of High Adventure PCA results, I'd built a nMonte analysis before where I used Yamnaya (Samara), Iberia_Chalcolithic, Iberia_EN, Tepecik-Ciftlik_Neolithic, LBK_EN, Germany_MN (Baalberge + Esperstedt) to try and model recent Europeans. That gave me interesting results with very geographically concordant peaks (e.g. German MN peaks in Germany, Iberia Chal in Basques, etc.), but gave some odd results for Bronze Age steppe picking up Chalcolithic Iberian.
I tested whether adding LN1 to this set helped, but unfortunately for my method, this doesn't make it go away, e.g.
Basque_French: Iberia_Chalcolithic - 82.75, Yamnaya 17.25 - distance% = 1.6718 %
Norwegian: Latvia_LN1 - 60.45, Iberia_Chalcolithic - 39.55 - distance% = 1.1628 %

English_Cornwall: Iberia_Chalcolithic - 31.7, Latvia_LN1 - 31.6, Yamnaya - 19, Germany_MN - 17.7 - distance% = 0.7819 %
German: Germany_MN - 41.35, Latvia_LN1 - 38.1, Yamnaya - 14.85, Iberia_Chalcolithic - 5.7 - distance% = 0.6493 %
Hungarian: Latvia_LN1 - 46.4, Germany_MN - 40.15, Yamnaya - 9.4, Tepecik-Ciftlik_Neolithic - 4.05 - distance% = 0.9156 %

Polish: Latvia_LN1 - 72.1, Germany_MN - 27.9 - distance% = 1.6592 %
which all make a kind of sense, but...
Corded_Ware_Germany: Yamnaya - 54.25, Iberia_Chalcolithic - 23.45 Latvia_LN1 - 22.3 distance% = 0.7328 %
Bell_Beaker_Germany: Iberia_Chalcolithic - 43.1, Latvia_LN1 - 33.35, Yamnaya - 21 Germany_MN - 2.55 - distance% = 0.3049 %
Hungary_BA: Latvia_LN1 - 50.8, Germany_MN - 44.6, Iberia_Chalcolithic - 4.6 - distance% = 1.811 %

Sintashta: Yamnaya - 55.55, Iberia_Chalcolithic - 29.55, Latvia_LN1 - 14.9 - distance% = 0.9392 %

So LN1 seems kind of not as useful as I had hoped it might be in reconciling the problem I had with these analyses for ancient individuals picking up excess of Iberia_Chal that throws some doubt on things.

Rob said...

@ Chad
Why do you propose that BB has no CHG if it derives from Yamnaya (for which everyone agree had ChG)?

Shaikorth said...

Adding SNP's revealed the ANE in Ukraine_N compared to the HG:

Mbuti MA1 Loschbour Ukraine_HG1 0.0114 0.936 447952

Mbuti MA1 Loschbour Ukraine_N1 0.0510 4.179 439711

Yet additional SNP's show no Kotias even when compared to Bichon, in fact the D value goes down too.
Mbuti Kotias Bichon Ukraine_HG1 0.0054 0.494
Mbuti Kotias Bichon Ukraine_N1 0.0057 0.551

Chad Rohlfsen said...

I didn't say no CHG. I said little. That's why Khvalynsk is a better admixing source than Yamnaya.

Those stats with Ukraineca hair closer to CHG is that CHG is like EHG, plus Basal Eurasian. It's about the non-Basal in CHG, and not CHG in Ukraine. If they had 10-15% CHG it would be significant.

Chad Rohlfsen said...

Are closer. Sorry, autocorrect on the phone.

Chad Rohlfsen said...

I'll bet EHG is closer to CHG, which will also show my point. I'll get to all this when I'm up and running. Making geno output now. Give me a bit.

Davidski said...

My qpAdm model suggests that there may be some CHG in Ukraine HG/N. But keep in mind I'm only using 9,000 SNPs here. So take from this what you will.

Ukraine_HG/N
Caucasus_HG 0.177±0.081
Eastern_HG 0.576±0.110
Western_HG 0.247±0.120

chisq 6.574 tail_prob 0.832496

On the other hand, there's no need for CHG when modeling Latvia HG. In fact, the model fails if I try it. Using almost 35,000 SNPs for this though.

Latvia_HG
Eastern_HG 0.288±0.040
Western_HG 0.712±0.040

chisq 6.886 tail_prob 0.865047

Romulus said...

Guys it's looking like PIE warrior women rode out from Anatolia with bronze weapons, killed off the indigenous mtDNA U4/5 women, and took their men. Calling it now, please refer to me as Romstrodamus.

Davidski said...

No, a small number of steppe men of forager origin ran out of local women for wives and girlfriends, and started taking women from nearby farmer villages. So nothing's changed with these results.

The really interesting thing is that the Latvian Corded Ware looks mostly like a mix of Ukraine HG and CHG, and so do German Corded Ware, except with more Anatolian/EEF stuff.

So I won't be surprised if those Ukraine HGs are shown to belong to R1a, and for proto-Corded Ware to have expanded from where they were sampled.

Rob said...

Whatever their ultimate locale, it was a very opportuned switch from hunte_gatherers, with a 1000 year of selective agro-pastoral uptake to then a switch to cattle herding specialism. The lattera origin is actually to be found in MNE Europe - Baden and the likes, with the steppe adapting it through the 1000 years of reciprocity. Then, for some reason Baden collapses and even Cernavoda - Usatavo (practicing their own brand of mostly sheep pastorliasm) are overlaid by Yamnaya. But the important thing to note is that this happened c. 2600 BC, not 4000 BC.
As such; I subscribe to a "hyper-recentist" (my own terminology) chronology for the breakdown of PIE- as late as mid 3rd Mill BC when the PIE dialects began to disattach .
I have theories on Myceneans but will pause for now

Romulus said...

I don't think it's that they ran out of women, that's a silly suggestion. They probably traded their goods to the farmers for women, domesticated animals, metal tools, etc. EEF women were high status objects in the HG tribes (Chief's wife) and over time the advantage that comes with being the Chief's offspring leads to a disproportionate rise in EEF (or in the east CHG) autosomal.

Rob said...

@ Ric Hern

Read (should be able to find on academia.edu)

"The Latest Epigravettian Assemblages
of the Middle Dnieper Basin (Northern
Ukraine)"


"The Early and Mid-Upper Palaeolithic of the
North Black Sea region: an overview"

Then we can clarify things

Davidski said...

@Romulus

Without a law enforcing monogamous marriages, high status men took more than one wife, and often a lot of wives. This left other men with no choice but to fight at home or abroad to gain status and wealth to get a wife.

This happened in Viking-era Scandinavia, and it looks like it happened on the steppes, triggering expansions or clan wars, and probably Y-hg turnovers, like from R1b to R1a on the Caspian steppe.

Romulus said...

@Davidski

That isnt a trait specific to Steppe people though. It's something ubiquitous in all human societies and even in primates. It doesn't explain why a farmer wife would be any more or less desireable than a HG wife, why we see the increase in farmer mtdna groups and the drop off in HG groups. Some type of wife kidnap scenario would make the kidnap wife marginalized in that society and if anything and would decrease reproductive success of that lineage within it.

I see the indo-europeanization process as a peaceful acculturalization from farmer to native, although patriarchal in nature and at the expense of local women. That hinges on R1b natives and we're finding them now.

Only when that process is complete do we see these people expand like the farmers over wide areas, and in an explosion of Y DNA subclades. As each tribe was indo-europeanized by the farmers they underwent a massive population explosion and spread into areas inhabited by other natives not yet indo-europeanized.

Romulus said...

We know the farmers were of shorter stature, so while their technology gave them greater reproductive success, they weren't equipped to engage in physical violence with the natives. So they led a peaceful coexistence until that technological edge dissipated at which point they were simply swallowed up in later expansions.

Romulus said...

Like the stories of the Aesir and the Ice Giants or the Olympians and the Titans.

Samuel Andrews said...

@Romulus,
"We know the farmers were of shorter stature, so while their technology gave them greater reproductive success, they weren't equipped to engage in physical violence with the natives. So they led a peaceful coexistence until that technological edge dissipated at which point they were simply swallowed up in later expansions."

Give me a break. If you've lived in the world you know all ethnic groups have huge variation in body build, features and rarely is one obviously physically superior to another. Have you read studies who detaildly analysed bones from Steppe and MN people and who concluded Steppe people were significantly physically superior?

You're adding personality to entire ancient populations. Sometimes culture/genes create personality traits for populations but we know hardly anything about these ancient populations. We know so little we shouldn't even play around with giving them personality traits.

Davidski said...

Farmer women weren't necessarily more desirable. There was just more of them around nearby than local women on the steppe.

And farmers weren't Indo-Europeans, because many farm-related words in Indo-European languages are of non-Indo-European origin. So it's the opposite to what we see with words related to things like war.

Davidski said...

Swapping Satsurblia with Iran_Neolithic in the right pops, and adding Satsurblia to CHG, just to make sure, and trying two different models, with and without CHG. The fit is better with CHG, but not much better, so I'd say Ukraine HG/N probably has minor CHG. This is based on 11,000 SNPs.

In any case, I wouldn't dismiss the notion that Ukraine HG/N has CHG ancestry based on some D-stats, because D-stats are a really chunky way to look for admixture signals and often miss a lot of stuff.

Ukraine_HG/N
Caucasus_HG 0.125±0.094
Eastern_HG 0.588±0.108
Western_HG 0.288±0.103

chisq 4.933 tail_prob 0.895611

Ukraine_HG/N
Eastern_HG 0.659±0.096
Western_HG 0.341±0.096

chisq 6.690 tail_prob 0.823614

Romulus said...

@Sam

I base farmer and hunter gatherer coexistence based on a lot of papers about it. This one is very good:

http://www.academia.edu/1469446/Interaction_between_hunter_-_gatherers_and_farmers_during_the_Neolithic_in_Poland

And also, yes I have read a lot of works about how Gracile Farmers were smaller in stature than their Cro-Magnoid counterparts.

Likewise we have Modern Europe to go off of in which there is a direct correlation between WHG DNA and greater stature, as well as what we already know about Steppe people, Hunter gatherers, Farmers and height. It's a fact, you don't seem to like it from which I can only assume you are a shorty yourself LOL.

@Davidski

There's just as much lingustics crap out there supporting the farmer hypothesis as the steppe. Linguistic study will always be inconclusive so why even bother.

http://language.cs.auckland.ac.nz/

a said...

"This happened in Viking-era Scandinavia, and it looks like it happened on the steppes, triggering expansions or clan wars, and probably Y-hg turnovers, like from R1b to R1a on the Caspian steppe"

IMO modern day Scandinavia[ydna-turnover] might be a better example.

Below is a map of R1a-Z93/Sintashta/Arkaim aka " The Badass Lands" They built fortified defensive forts; complete with moats. Had choice metal weapons, and invented war chariots. Their is a R1-z93 shadow on the Caspian Steppe. If they were not able to make a defense; then who could?
https://lh3.googleusercontent.com/-75LFC2DbVTQ/U0pzZpEe2QI/AAAAAAAAAU4/-KnlCxo9SkM/w746-h408-no/Underhill_Z93.png

Do you know the ydna most represented in Caspian Steppe? In particular Sintashta/Arkaim region?
http://bsecher.pagesperso-orange.fr/genetique/R1b-M73.jpg

Samuel Andrews said...

I'll create interesting posts about European mtDNA at my blog in the next few months and most will be about Europeans' ancient mtDNA ancestors(MN/EEF/Middle Eastern/NW African) mtDNA to some degree.

Thus far the evidence does suggest Steppe ancestry is mostly male mediated and EEF ancestry mostly female mediated. EEF is by far the biggest mtDNA contributor to modern Europeans. If we judge Steppe mtDNA percentage according to U5a/U4 frequencies(hgs EEF had basically 0% of); Northern Europeans and Balkanerers have only 20-30% Steppe mtDNA despite some having maybe 40-50% Steppe ancestry.

Rob said...

@ Davidski

If D_stats are too 'mass' for finer detail, then this is what I get with nMonte. I tried normal, unweighted, and weighted values (care of Alberto). The results were within a few of each other - very similar.

Ukraine HG:
Villabruna: 62%
Afantova: 25%
Kotias 13%

Ukraine Neol.
Villabruna/Bichon: 60%
Afantova: 29%
Kotias:11%

Latvia_HG:ZVEJ25
Bichon:87%
Afantova: 10%
Kotias:3%


Latvia LN:
WHG:43%
Kotias:48%
Afantova:9%


Full details, and others, http://i.imgur.com/XPLdsPZ.png

Davidski said...

@a

Do you know the ydna most represented in Caspian Steppe? In particular Sintashta/Arkaim region? http://bsecher.pagesperso-orange.fr/genetique/R1b-M73.jpg

Yeah maybe, but not among the Late Bronze Age elites buried in Kurgans.

This is not an R1a vs R1b thing. Some steppe clans may have had R1a-Z280 and fought other clans with R1a-Z93, or there may have been R1b-L51 vs R1b-Z2103 scuffles.

@Romulus

You need to employ some sort of sanity check when formulating your theories, because right now they sound plain crazy.

The whole farmer, or rather farm girl, angle looks like the classic definition of special pleading.

Romulus said...

@Davidski

From my perspective the steppe theory is special pleading from slavs with an inferiority complex.

Samuel Andrews said...

@Romulus,

Ok you do have some sources. Fair enough. I'm still really skeptical about any sweeping conclusions about ancient peoples we don't know a lot about.

Davidski said...

@Romulus

You're the one with the inferiority complex here, a G2-insipred Neolithic farmer one, which is hilarious.

Thanks for the comic relief and all, but do realize we're all laughing at you, not with you.

Rob said...

@ Romulus

Based on ethnographic studies, anthropologists argued that it was hunter-gatherer women which were brided to farming communities. On the other hand, a farmer's whole family might move out of their community for new opportunities, or if they are a subsidiary lineage, beyond the frontier, taking their skills and knowledge with them (eg farming, or metallurgy).
However, this theory might not hold for the European LNBA, as it seems hunter-gatherer lineages came to dominate.

Rob said...

@ Sam

" I'm still really skeptical about any sweeping conclusions about ancient peoples we don't know a lot about. "

Scholars have been studying the steppe groups and Neolithic groups for over 100 years, and we know a lot about their social structure and economy. aDNA is the icing on the cake.
It seems Kossina and even Coon were right about a lot of things.

Romulus said...

@Davidski

I don't belong to G2a if that's what you're thinking but I do truly think the farmers were special and it's a fact. Everywhere on earth were hunter gatherers whom were more or less flora and fauna (if you go by colonial british definitions) until that first spark of genius led to the farming switch and humanity gained an entirely new survival vector which put us here where we are today.

The Megalithic monuments they created stand as a testament to that. The succeeding cultures did nothing to further the technology they got from the farmers until romans and greeks chock full of EEF arrived on the scene again.

I think this video explains my view:
https://www.youtube.com/watch?v=czgOWmtGVGs

Davidski said...

Yeah, you're fucking crazy. Hilarious, but crazy nonetheless.

rozenfag said...

Questions: second paper about Baltic Mesolithic DNA: will it include samples from Estonia/Latvia/Lithuania only or there could be samples from another regions?

Rob said...

ELL only

Rob said...

I think what we're going to find is that all these emerging individuals from around eastern Europe contributed to make the so-called "EMBA steppe migrations", to different degrees in individuals. In other words, it wasn't all from one specific spot.

Eg
Yamnaya Kalmykia RISE 552
Samara Eneolithic: 37.4%
Kotias: 33.6%
Latvia/Ukraine/ Karelia HGs: 25%

Yamnaya_Samara II0357:
Samara Eneolithic: 65%
Kotias: 14%
Baden:9%
Latvia HG: 6%
Latvia MN:6%

So local Samara Neolithic played dominant role in Yamnaya.

But take a look at BB:

BBGermany I0108
Latvia HG:21%
LBK: 42 %
Samara_Enol.:13%
Kotias: 9 %
Latvia MN: 21 %

BBCzech RISE568:
Latvia_HG:52%
Lengyel:29%
Kotias 18%

CWC Estonia:
Latvia_HG:35%
Baden_C01: 25%
Samara_Enol: 23 %
Kotias:11%

BattleAxe RISE94
Kotias:29%
Lengyel:21%
Ukraine_HG:20%
Ukraine_Neol: 12%

PL_N17
Latvia HG:36%
Kotias: 29%
LBK: 17%
'Eastern_Eneol':16%

I think a tentative case might be made that Yamnaya and BB indeed do have distinguishable origins.

Samuel Andrews said...

@Rob,
"I think what we're going to find is that all these emerging individuals from around eastern Europe contributed to make the so-called "EMBA steppe migrations""

CHG/EHG ratios in LNBA Europeans wouldn't be so similar is that was the case. In every analysis I've seen so far Latvia_HG, Latvia_MN2, Ukrainian HGs, Motala HG are simply mixtures of WHG and EHG. So in tests WHG and EHG in later Europeans can be traded among those different ancestors and there's no precise way to differntaite Latvian HG, Ukrainian HG, Motala HG ancestry from ancestry from ancestors who were pure WHG and EHG.

Rob said...

Sam

I don't agree, because the results are consistent & reproducible, albeit dependant on what is added as source .
Just have a look- why is Samara Eneolithic the choice preferred from Yamnaya Samara, whilst more western choices for BB? When added with archaeological context and Y lineages, it might all fall into place, of course with outliers to be expected

Nirjhar007 said...

Dave,Alberto,Rob

I guess with different modes of modelling you do get different results . But is it now confirmed, that those Ukrainian samples are carrying CHG admixture?.

Rob said...

It is also now clear where the "hidden" WHG we disceased in earlier times appears from - Eastern Europe, somewhat ironically. It probably existed in a long strip from the Baltic to western steppe, carpathian and even parts of the northern Balkans

a said...

This is not an R1a vs R1b thing. Some steppe clans may have had R1a-Z280 and fought other clans with R1a-Z93, or there may have been R1b-L51 vs R1b-Z2103 scuffles.

It is interesting to see the Estonian R1b samples. From Khvalynsk-Sintashta-Estonia- burials[ R1A/B variance in clades] are stratified or in relative close proximity to each other. Not to many places that this is common other than contact with Pontic Steppe/Eastern Europe. regions/zones.

Rob said...

Nirjhar
Not much ~10% . But the latest one is only from 4200 BC, about the same time as Khvalynsk.

Davidski said...

@Nirhjar

I guess with different modes of modelling you do get different results . But is it now confirmed, that those Ukrainian samples are carrying CHG admixture?.

Probably, but don't over interpret this if the Ukraine HG are confirmed to belong to R1a.

R1a did not arrive in Eastern Europe with CHG or Iranian farmers. R1a is forager lineage native to Eastern Europe.

Nirjhar007 said...

Thank you Rob, Dave . So this is an exciting development , the CHG they are carrying is likely to be genuine . Perhaps it is time , to change the idea that CHG came entirely from female exogamy , which did sound superficial from the start !.

Rob said...

I guess it'll depend on which Y lineages there were in Majkop.

Davidski said...

No one ever said that gene flow from the Caucasus onto the steppe was entirely female mediated. J1 was found in a Mesolithic context alongside R1a in Karelia remember. But it sure was largely female mediated, especially during the Copper and Bronze Age, when steppe clans carried entirely R1a and/or R1b.

This is what I said ages ago...

http://eurogenes.blogspot.com.au/2015/11/fourth-strand-of-european-ancestry.html

Nirjhar007 said...

Dave,Rob
I think CHG as shown increasing with time , must be connected with some kind of language shift as well , though genetic-linguistic evolution is by no means needed to be unidirectional .

Anyway, at the end I am more interested on R1a-M417+ and R1b-M269+ and there are some massive papers coming ...

Samuel Andrews said...

@Rob,
"It is also now clear where the "hidden" WHG we disceased in earlier times appears from - Eastern Europe, somewhat ironically."

There's no convincing evidence Latvian HG, Ukrainian HG, Yamnaya contributed ancestry independently to Europe. There's no convincing evidence Ukrainian HG rich Steppe populations who were therefore rich in WHG are a source for WHG ancestry in Europe.

Many here for some time now have thought some WHG in Europe is from Eastern European hunter gatherers who mixed with MN farmers and Yamnaya like Steppe people. Ever since we got Yamnaya, MN, and Hungary HG genomes we've thought there Mesolithic Eastern Europeans were WHG-rich.

Davidski said...

Well, crazy man Genetiker is at it today, and voila, I2a2a from Mesolithic Ukraine and R1a from Neolithic Ukraine.

https://genetiker.wordpress.com/2017/02/04/y-snp-calls-from-mesolithic-and-neolithic-latvia-and-ukraine/

So, mystery of the Corded Ware pretty much solved, unless of course Genetiker is way off. But he probably isn't. He's just nuts, but he can call Y-SNPs well enough.

Should be interesting to see what Latvia LN Corded Ware is. Almost certainly R1a, but which subclade?

Romulus said...

lol looks like 1 is r1a1 and 1 is i2a2

Romulus said...

I don't see M269 Chad.

Romulus said...

these results don't seem relevant

Rob said...

@ Dave

"Should be interesting to see what Latvia LN Corded Ware is. Almost certainly R1a, but which subclade?"

All/ most German CWC was Z645 - L664+, so I wonder if Baltic & east Polish R1a was Z280+ already ?

Davidski said...

Yeah, I reckon it'll be Z280. 90% probability IMO.

EastPole's model showing Latvian CWC as an Ukraine HG/N and CHG mixture was spot on.

Chad Rohlfsen said...

Lol. R1b will come. Wait for the next paper.

capra internetensis said...

Latvia_LN1 is a woman.

This R1a is considerably further from R1a-M417 than Karelia_HG is, so I don't see that it points to the steppe for the origin of the latter. But is evidence of now lost basal diversity in the area

No surprise that Latvia_MN1 is also P297. Could be early pre-M73 or some real P297*.

Davidski said...

Ah, that's a bummer.

We gotta wait for the next paper in that case, with more samples from Baltic Corded Ware and Ukraine.

It's on it's way, and it would be pretty amazing if R1a-M417 wasn't from the proto-Corded Ware from the steppe.

capra internetensis said...

Scratch Karelia_HG being closer, I was mixing it up with the Smolensk results (if those are real). Should have double checked.

Rob said...

@ Dave

"EastPole's model showing Latvian CWC as an Ukraine HG/N and CHG mixture was spot on"

Perhaps, but what is that based on (apart from arrows) ?
Because the optimal fit for Latvia CWC I get is:

Latvia_LN1:ZVEJ28
Latvia_HG:ZVEJ32 44.2 %
Kotias:KK1 35.65 %
Samara_Eneolithic:I0434 19.85 %
Ukraine_HG1:StPet2 0.3 %



Davidski said...

You're probably overfitting though.

Rob said...

In what way ?

Davidski said...

Too many individual samples with high correlations between them.

Rob said...

But then if you model on the basis of exclusion with a priori models in mind, then it's not really an independent test . If you include both Latvian Hg and Ukraine HG, it might be overfitted but at least it's the objective choice

Samuel Andrews said...

One Yamnaya had typical WHG mtDNA U5b2a1a. Another had typical WHG Y DNA I2a2a. It seemed weird to me at first because I thought there weren't WHGs so far east. But now we have prove both existed in Ukraine 11,000 years ago and that can easily explain their presence in Yamnaya.

Looks like Eastern Europe and Scandinavia were a WHG/EHG mix, with both WHG yhg I, EHG yhg R1.

@Davidski,

You should probably first thoroughly test if Corded Ware Germany fits as part UkraineHG/N ancestry before concluding Corded Ware Germany's R1a is from Ukraine. R1a existed in Karelia but Corded Ware isn't from Karelia.

Davidski said...

@Rob

But then if you model on the basis of exclusion with a priori models in mind, then it's not really an independent test . If you include both Latvian Hg and Ukraine HG, it might be overfitted but at least it's the objective choice.

It's not an objective choice. It's biased by the methodology.

You need to look at other data, like PCA, come up with a plan, and be more prudent with your methods.

Where does Latvia LN cluster on the PCA? Why does it cluster there?

Why is Latvia LN so similar to Yamnaya and Corded Ware? Because it formed independently from similar ancestral groups? Nonsense. Latvia LN is straight from the steppe. Was there any Latvian HGs on the steppe? Nope.

Rob said...

Dave

No there weren't Latvian HGs on the steppe, but there clearly was a WHG - EHG continuum in places like the Ukraine steppe and east Baltic.
Moreover, how do you know that every CWC male came from the steppe ?

Davidski said...

I never said that every Corded Ware male came from the steppe. I've always said that the early Corded Ware population expanded from the steppe.

Latvia LN looks like a new, foreign introduction to the Baltic from the Pontic Caspian steppe. Hence, its primary ancestral populations should be sought on the steppe.

Ukraine looks like a good place, and the Ukrainian samples, although low quality, do fit the bill, especially since we now know that one of them belongs to R1a.

Rob said...

We know that CWC probably expanded from somewhere in Ukraine
But if this *particular individual* is an "acculturated local", the best match for him might be the Latvian HG. I'm sure some R1a existed here too .

Aram said...

I guess if we have CWC samples from Bielorussia they will also lack EEF. Or will have low level.

Samuel Andrews said...

@Davidski,

Using the PCA locations you provided here...

http://eurogenes.blogspot.com.au/2016/11/days-of-high-adventure.html

Corded Ware Germany favors EHG and Yamnaya over Ukranian HG/N and LatviaLN

CWC Germany Avg
"Samara_HG:I0124" 40.85
"Esperstedt_MN:I0172" 25
"Kotias:KK1" 22.95
"Loschbour:Loschbour" 11.2
"Ukraine_HG1:StPet2" 0
"Ukraine_N1:StPet12" 0

CWC Germany Avg
"Yamnaya Samara Avg" 64.95
"Esperstedt_MN:I0172" 23.6
"Latvia_HG:ZVEJ27" 11.45
"Latvia_LN1:ZVEJ28" 0
"Ukraine_HG1:StPet2" 0
"Ukraine_N1:StPet12" 0

Yamnaya though can be modeled as largely UkrainiaHG/N. When Corded Ware Germany is modeled as Ukraine/N, MN, CHG the MN score rises and the CHG decreases to unrealistic levels. MN absorbs CHG.

UkraineHG/N explaining the extra WHG in LNBA Europe and modern Europe though makes sense.

Davidski said...

But if this *particular individual* is an "acculturated local", the best match for him might be the Latvian HG.

No, obviously Latvia LN is just a variant of Steppe EMBA.

Rob said...

I think you're approaching things too simplistically Dave

Samuel Andrews said...

HungaryBA's nMonte results from the PCA data I just mentioned gives it a big chunk of UkrainHG/N-type stuff. We've noticed for a while it has lots of EHG but not lots of CHG, which UkraineHG/N could explain.

Hungary_BA:I1504
Hungary_CA: 58
Ukraine_N1: 23.65
Yamnaya Samara Avg 17.15

Hungary_BA:I1502
Hungary_CA: 54.3
Ukraine_N1: 38
Loschbour: 8
Yamnaya_Samara Avg: 0

Hungary I1502 had a big chunk of WHG ancestry and can maybe explain unexpected high WHG in modern Europe. I used David's Global10 PCA for the following nMonte results.

I'm just throwing hypothetical models. I agree with you guys, Rob and David, that maybe extra WHG spread to Europe from the east(Ukraine, Hungary).

distance=0.005593"


Polish
"Hungary_BA:I1502" 54.8
"Corded_Ware_Germany:Avg" 42.95
"Esperstedt_MN:I0172" 2.25

distance=0.00263"


Polish
"Corded_Ware_Germany:Avg" 44.55
"Esperstedt_MN:I0172" 32.65
"Ukraine_HG1:StPet2" 22.8
"Hungary_CA:I1497" 0
"Ukraine_N1:StPet12" 0

distance=0.004959"


Norwegian
"Corded_Ware_Germany:Avg" 49.2
"Hungary_BA:I1502" 38
"Esperstedt_MN:I0172" 12.8

distance=0.003008"


Norwegian
"Corded_Ware_Germany:Avg" 49.85
"Esperstedt_MN:I0172" 33.95
"Ukraine_HG1:StPet2" 16.2
"Ukraine_N1:StPet12" 0

Azarov Dmitry said...

@Davidski
It's on it's way, and it would be pretty amazing if R1a-M417 wasn't from the proto-Corded Ware from the steppe.


It wasn’t. I’ve already explained you everything in your post from September 11, 2016 (ASHG 2016 abstracts)
-------------------------------------------------------------------------------------------
Azarov Dmitry said...
@Davidski
How will that change the fact that Corded Ware cluster close to Yamnaya and look like over 70% of their ancestry is from Yamnaya? I don't see how unless some of those Balkan farmers are basically Yamnaya.

But of course they're not basically Yamnaya. I can tell you that Corded Ware colonized most of Eastern Europe from the steppe, and the people living today in most of Eastern Europe are largely of Corded Ware origin. You can take that to the bank.




It’s a bit more complicated. First of all Corded Ware culture is a result of expansion of mostly western part of Yamnaya culture (Sredny Stog population (mostly R1a-YP1272) transformed as a result of cultural contacts with Maykop population (R1a-M417)). Secondly ancestors of the people living today in Eastern Europe came not from Yamnaya (first wave of migrants) but from Maykop -> Catacomb cultures (second wave of migrants).

Distribution of main R1a subclades in Eastern Europe by 3000 BC

http://s017.radikal.ru/i419/1609/b1/8ccb18c49f10.jpg

Distribution of main R1a subclades in Eastern Europe between 2900 – 2700 BC

http://s019.radikal.ru/i616/1609/aa/0af2b75656c3.jpg

Distribution of main R1a subclades in Eastern Europe between 2700 – 2200 BC

http://i056.radikal.ru/1609/dd/d77e91e56b77.jpg
September 11, 2016 at 6:34 AM

Rob said...

Sam

Run all CWC separately
Run all BB separately . Also throw in battle axe and Nordic LNBA (but you'd have to use the PCA data)
You will see there are variations in individuals because not everyone came from the same patch of land
Aside from expected variation, eg due to taking different wives from an SHG, or german MNE, you might find true outliers

Samuel Andrews said...

@Rob,
"I think you're approaching things too simplistically Dave"

LatviaN is a Eastern European HG(probably UkraineHG) and Caucasus HG mixture. EHG had existed in Latvia earlier but CHG hadn't. Even if we didn't have Yamnaya genome, geographically speaking it would make the most sense to say LatviaLN was orignally from land southeast of Latvia close to the Caucasus mountains.

Samuel Andrews said...

UkraineHG/LN and Latvian HGs definitely complicate European genetics. They show us EHG could be older and more diverse than we thought before. They show us modern European genetics might be more diverse than we thought before.

For instance, modern Irish and modern Ukrainians' EHG might come from EHGs who were isolated from each other for 1,000s of years. The same could be true for their WHG, CHG, EEF ancestors. Ukrainians and Irish could have become a fairly similar mixture in very different ways. I think we or at least I simplified and unified European genetics. Plus unknown Southern Europe received unknown West Asian migrations, which diversifies European genetics even more.

Rob said...

@ Sam

"Even if we didn't have Yamnaya genome, geographically speaking it would make the most sense to say LatviaLN was orignally from land southeast of Latvia close to the Caucasus mountains."

Not quite. It would mean part of the Latvia MN was from the southeast, not the totality of the individual in question. And that new part was the chg. it's not out of the question to suppose exogamy happenein even to the far off Baltic. Amber, fur and all

Alberto said...

@Chad

I didn't say no CHG. I said little.

It's sometimes hard to know to whom or to what you are replying. I posted numbers of Ukraine_HG having 11-12% CHG and you said that this method was creating ghost CHG. It would be good if you quoted or addressed with @whoever your comments.

In any case, I await your own analysis to confirm or deny that Ukraine had CHG admixture.

@Shaikorth

Yes, but when 2 stats, one with transversion sites and one with all the sites don't agree, you can't say that stats show that there is no CHG in Ukraine. You have to say that stats are inconclusive, so we need further investigation. That further investigation implies this IBS based PCA, qpAdm, other D-stats to check for basal Eurasian admixture, etc... Probably the evidence will continue to support the stats I posted and some CHG admixture (but let's see, the more data the better. We all want to know with the highest possible certainty).

@Sam

UkraineHG/LN and Latvian HGs definitely complicate European genetics. [...] I think we or at least I simplified and unified European genetics.

I'm very glad you admit this, and I hope you remember this words for the future. It's not nice to go around calling people rebels or idiots because they doubt the most simplistic conclusions based on partial data (especially when those people know a lot of things that you don't, and they have their reasons to doubt those simplistic conclusions). This increased complexity is probably only the beginning. We're all learning new things here every day, let's keep things civic from now on.

Nirjhar007 said...

They give R1b1a to Latvian HG3 (but where is HG2? maybe confused with MN1?) .

About R1b, I was thinking that the only solution is that it appeared in West Asia before the migration of HGs to (Eastern?) Europe. Also they came from West Asia, originally .

Shaikorth said...

f3-stats in the paper show that both Ukraine_N and basically hunter-gatherer Latvia_MN2 share a similar amount of drift with Onge, and more drift with Onge than with Yemenis. Latvia_HG's 2 and 3 show the same pattern, while Latvia_LN shares more drift with Yemenis than with Onge. If Ukraine_N had CHG it probably should share less drift with Onge.

Nirjhar007 said...

About Ukraine N1: "The skeletal remains used in our genetic analyses ((skeleton 2; 14C date: Poz-83446, 5590 ±50 BP, 6,469-6,293 cal BP) came from a single burial located within the main core of burials. This individual was buried in extended supine position in north-south orientation."

This is quite different than of the burials , we see in CWC.

Ric Hern said...

Thanks Rob.

Alberto said...

@Shaikorth

Maybe. The quality of the samples is not great, apparently, and you're looking at a graphic with coloured dots, not even numbers or population names. You can also look at the dot above Yemen (Saudis?), and check that Latvia_MN1 and Ukraine_HG1 share more drift with them than Lavia_HGs do.

Latvia_LN1 is a different case, with over 40-45% CHG admixture. When we're talking about 10-12% it's much more difficult to see the difference.

Let's see what others come up with.

Matt said...

There are distinctions between the different EuroHG samples on a number of the dimensions in Days of High Adventure PCA.

http://i.imgur.com/nxe0def.png

This includes the dimension 6-7, which shows a comparatively clearer East-West European structuring and contributes to firm up connections between populations who are more separated on dimension 1-2. (Although to be honest, even dimensions 1-2 of DoHA seem to produce more logical between population distances on fine structure between West Eurasians lacking substantial non-West Eurasian admixture than using all dimensions of Globe10).

In general the West EuroHG (France, Germany) samples seem on the West end and East EuroHG (Ukraine) on the East end. it's not totally clear, and some samples have extreme and non-geographical positions so I wonder if that is not spurious.

The dimensions where the EuroHG samples are more together seem to be generally those differentiating CHG from IranN and Kotias

http://i.imgur.com/OuwaaGx.png

Shaikorth said...

@Alberto

Those colours correspond to f-stats so comparison is easy based on that. Onge is the only Andamanese sample in the set so it's easy to locate, and Yemenis are the most basal+ssa sample. Their relationship is the easiest way to figure the relative levels of basal in that graph. The sample above Yemenis is either Yemenite Jews or Saudis, who have higher Euro-HG related ancestry and complicate the comparison.

Ukraine_HG1 has higher shared drift with everyone (scale runs from 0.22 to 0.27 instead of 0.21 to 0.26 like most samples) so that's not directly comparabe. Latvia_MN1 has the same Onge/Yemen pattern as MN2 etc.

Rob said...

With regard to the Latvian MNs, i think it is the female which is EHG, whilst the male R1b P297 is essentially WHG.

Gioiello said...

@ Shemuel @ Nirjhar007

But what does happen? Whereas Sam (an opponent of mine as all people of his Gattung) is realizing that he was wrong in pretty all he thought and seems giving reason to me in many things, you, Nirjhar007, who were one of the few friends I got in the blog, are coming back to your Euphratians?

"About R1b, I was thinking that the only solution is that it appeared in West Asia before the migration of HGs to (Eastern?) Europe. Also they came from West Asia, originally"

Did some of your PhDs from Stanford or Harvard send you some R1b aDNA from Middle East?
Are they the followers of Nostradamus or new King Midas who learned changing hg. E into hg. R1b?

Matt said...

Using a secondary PCA on the Days of High Adventure PCA data and limiting to Europe, Russia and modern European clusters*:

http://i.imgur.com/rqePk8M.png

Some arguable pattern there in PC3 where there is a Ukraine/Latvia HG polarity vs Russia HG+otherEuro HG polarity, and this aligns with SW Europe vs NE Europe. This is a small dimension though.

*Clusters 1-8 are European clusters and 9-10 came out for Middle East and Caucasus+Iran+Turkey.

Rob said...

@ Matt

Sorry I'm probably reading it wrong, but the polarity looks like Ukraine/Russia vs Latvia and other Euro, or is it something relative ?

Matt said...

@ Rob, on the PC2 it's like that. (The image file I posted has three images of PCA vertically in case it didn't look like that, first is 1 by 2, 1 by 3, 1 by 4.)

Then on the PC3 the EHG are on one end with Latvia, SHG and Ukraine HG on the other and then the European HG spread across the PCA (with no clear pattern - La Brana, Falkenstein, Racho88, Continenza, BerryAuBac on the EHG end and Hungary_HG, Loschbour, Rochedane, Chaudardes on the Latvia/Ukraine/SHG end).

Nirjhar007 said...

Ratna,

I am not sure about 'shemuel' ;), but I AM still your friend and will remain to be your friend in the future . But I consider, that friends also let other friends speak their opinions, even though they may disagree .

epoch2013 said...

@Rob

Would you be so kind to check if this unknown WHG in Dutch you recently mentioned, sometimes caught by Yamnaya and KO1 and sometimes by Loschbour IIRC, could be related to these HG's?

Gioiello said...

@ Nirjhar007

I didn't doubt about your friendship and I thank you, but do you really think that R1b has something to do with Middle East after not having been found there in aDNA and with all what is appearing in Europe, which, it seems to me, is perfectly in line with all my hypotheses? Also this R-M73(-M478 very likely) whereas R-M73* (the ancestral) is only in Western Europe? Did you read all what I wrote About R-V88? But we have also R-M335 (also in Germany) etc etc

Ariel said...

Takeaways

1) There is big chance that modern R1b came from WHG in eastern europe
2) There is big chance that some (or a big part) of the ANE/EHG admixture in eastern europe is from pre bronze-age invasion groups.
3) Both BB and CW might be more "native" than we previously thought.

Matt said...

@Ariel, more specifically I'd add that LN1 clarifies how early Corded Ware might have been autosomally different from to Yamnaya and how the later CW in Europe were different from Yamnaya+EuropeanMN. (More samples needed).

Re:#2 yeah, although I would temper expectation that it might be best not to get too carried away - the Baltic / Eastern European groups who were non-Neolithic and pre-Bronze Age invasion, although look like they were more persistent than HG in the West, were still likely to have been numerically pretty small compared to the influx of Bronze Age herders (though these possibly more from Corded Ware Russian forest zone rather than Yamnaya Pontic Caspian steppe?).

Still, it seems like possibly as there might be some mild degree to which populations in Eastern Europe today are closer to UkraineHG / UkraineN1 / LatvianHG than would be expected from their general position on the WHG-EHG axis (and relatively further from Samara and Karelia HG and Western European HG). Reversed for populations who look like all the EHG like ancestry comes from EHG / Yamnaya. But looks to me quite subtle if real.

Grey said...

@Romulus

"It doesn't explain why a farmer wife would be any more or less desireable than a HG wife, why we see the increase in farmer mtdna groups and the drop off in HG groups."

Desirable or available?

If you read about the horse-based pastoralists in the Sahel like the Fulani you can see a model for this.

Bride-price is in livestock, the livestock are all owned by the chiefs so the chiefs have all the wives. Young men inherit wives when their uncles, fathers pass on.

If they can't wait they group up and raid neighbors for cattle to pay a bride price or for wives directly so you'd get a situation where the top guys from population A would be having A/A kids and *some* of the younger men having A/B kids with women taken in raids from population B.

(plus some chief-chief alliance marriages across the border)

This seems like a plausible model to me.

(If correct the scale of this would be proportional to the raiding potential so if you had enough dna over a time sequence you'd start with very little chg mixture and it would go up over time.)

Amanda S said...

This isn't about the mixing of hunter gatherers and farmers. First there was the creation of a new way of life north of the Caucasus, a mobile form of pastoralism herding animals which had been domesticated in the near east and the horse which was domesticated somewhere on the Eurasian steppe. Once this new way of life had been developed, it had a tremendous expansionary potential due to the vast amount of land which was suitable for it. This is why polygamy was a good strategy for these pastoralists because, as they competed with one another to build the biggest herds and control the biggest territories, it allowed for a rapid expansion of their family groups. This is the context within which there was a need to bring in additional women from outside. The pastoralists in turn would have been able to offer the families of their Caucasus farmer wives a good bride price for them.

Davidski said...

@Ariel

2) There is big chance that some (or a big part) of the ANE/EHG admixture in eastern europe is from pre bronze-age invasion groups.
3) Both BB and CW might be more "native" than we previously thought.


How are you coming up with these estimates of big chances and big parts?

First of all, most of the foragers in the East Baltic and surrounds were very WHG-like, with only some pulling east as far as or beyond SHG. Secondly, forager population densities were very low, even in the East Baltic.

So do you know something I don't? Can you show me some data and models?

Richard Holtman said...

What the hell is wrong with being in Haplogroup G2a?

Romulus said...

Animal domestication wasn't invented on the Steppe, it was invented by Farmers, so before there was any herding of animals on the Steppe there was contact with farmers. They didn't domesticate their cattle, they got them from farmers. Polygamy wasn't invented on the Steppe either, unless it was and they somehow rode their horses down to the Congo and taught it to the Silverbacks there.

Polygamy doesn't lead to star like expansions in sub clades, it leads to bottlenecks, as per the Gorilla/Chimpanzee study I read. It's obvious when you do the math. It doesn't matter who is boinking them, 100 women produce 100 * (FERTILITY RATE) children. It can be 1 guy or 1 million guys. The fertility rate is the limiting factor and that is wholly dependent upon subsistence strategy. The subsistence strategy change coming from the HG -> Farming shift at end of the Neolithic. The mobile pastoralism thing is unimportant, was it a feature of the Yamnaya culture? Yes. Were the Yamnaya or Maikop ancestral to BBC or CWC? No. They were an offshoot on the Steppe contemporaneous to these cultures but not ancestral, what was ancestral was a synthesis of Farmers and HGs at the end of the Neolithic.

Rob said...

@ Epoch

Dutch
Hungary_CA:I1497 38.6 %
Latvia_HG:ZVEJ32 36.25 %
Kotias:KK1 23.1 %
Latvia_MN1:ZVEJ26 2.05 %

Davidski said...

What the hell is wrong with being in Haplogroup G2a?

Nothing.

But some people take it personally when it's pointed out that it's a farmer lineage that didn't do very well in the Days of High Adventure aka. Bronze Age.

Richard Holtman said...

Lol I'm in Haplogroup G2a and I'm proud of my farmer ancestry.

Richard Holtman said...

Just because a lineage is not Indo European doesn't mean that it is inferior....

Romulus said...

We don't know that G2a disappeared at the Bronze Age, we've got a fairly paltry amount of samples from a massive horizon. If 1000 farmers with G2a moved into Europe at the Neolithic with an indigenous population of hundreds of thousands of R1a/b and I1/2 hunter gatherers then the ratio has remained constant over time.

There is apparently G2a in Halstatt, G2a in the Alans, and G2a in Richard the 3rd. I think it's the European minority elite PIE lineage personally. We'll see with the Ancient Greeks and Romans had.

Davidski said...

Just because a lineage is not Indo European doesn't mean that it is inferior....

Not sure why you feel the need to emphasize this here?

Like I said, the issue is that this blog mostly deals with ancient DNA and the Bronze Age, because these topics are pertinent to European population history, which is what this blog is about.

But this frustrates and annoys a lot of people, particularly from Southern Europe, the Near East, and South Asia, because most of the action is on the Eastern European steppe or involves steppe people, rather than the ancient group that makes up the bulk of their ancestry.

Hence the crackpot theories, special pleading and more than the occasional hissy fit to try and shift the attention away from the steppe and steppe people.

Davidski said...

I think it's the European minority elite PIE lineage personally.

Case in point.

Richard Holtman said...

No this is starting to get to me are Indo Europeans (R1b R1a) superior to other Haplogroups?

Romulus said...

The entire R1a/b claim to fame seems to be being more frequent than the other haplogroups and hence feeling some sort of pride in that. But from what we can see in today's world the best people don't have the most kids and the relationship is quite the opposite. Within the framework of their own ideal they aren't the most frequent haplogroup on earth by a long shot so it's a generally stupid and self defeating source of pride. Likewise the areas of Europe with the greatest source of historical victory have an inverse relationship with these groups (Irish and Slavs high in R1b / R1a being dominated by Romans/Germanics high in EEF and I1 respectively. The theoretical Steppe migration would be the only source of historical victory for these people hence the dogmatic zeal they defend it with. The Steppe theory is really all R1a/b have going for it.

Likewise a lot of people who study this field have their own expectations about their ancestry based on historical anthropological works which includes Nazi race theory. I think what the Steppe theory boils down to is a lot of people expecting to be part of the Nordic Race turning out to be part of the Alpine Race and wanting to re-write their own "glorious history" in reaction.

But you only need to look at the sad states of Scandinavia and Ireland up until a thousand years ago in comparison to the Ancient Greeks/Persians/Romans to know that the spark of Greatness comes from the Farmers.

Rob said...

Every lineage and civilization had its heyday
Nothing necessarily inherent in quality

Richard Holtman said...

Yeah I agree Romulus they seem to think they are somehow superior and it's getting old real quick.

Rob said...

@ Epoch

Btw I'm very satisfied with that result . I don't think it'll change much

Samuel Andrews said...

@Davidski,
"Not sure why you feel the need to emphasize this here?"

Because you definitely show favoritism to Steppeness.

"But you only need to look at the sad states of Scandinavia and Ireland up until a thousand years ago in comparison to the Ancient Greeks/Persians/Romans to know that the spark of Greatness comes from the Farmers."

What? What about England and Germany? Anyways why even try to rank people according to their distant ancestry? There's nothing in their genes or slightly higher percentage of ancestry from people who farmed 8,000 years ago which affects their society's success.

This is apart of the same problem as believing, without a lot of data to analyse, that Steppe people were physically superior to MN.

Rob said...

@ Sam

Do you still think I2a2 expanded fr iberia ?

Davidski said...

Holy crap, I missed this gem from Azarov Dmitry.

It’s a bit more complicated. First of all Corded Ware culture is a result of expansion of mostly western part of Yamnaya culture (Sredny Stog population (mostly R1a-YP1272) transformed as a result of cultural contacts with Maykop population (R1a-M417)). Secondly ancestors of the people living today in Eastern Europe came not from Yamnaya (first wave of migrants) but from Maykop -> Catacomb cultures (second wave of migrants).

Dmitry, in regards to the staging point and culture for the expansion of R1a-M417 during the Copper/Bronze Age, I've got two words for you: Not Maykop.

Ariel said...

Davidski

Everybody can see what's going on here, we knew already that there is a differece in the CHG/EHG proportion in Yamnaya compared to CW or BB. You want deny that? Do you have a theory for why it is the case? Mine is simple.

Davidski said...

I suspect mine is even simpler than yours: CWC and BBC didn't come from the Samara or Kalmykia Yamnaya populations, but from very closely related groups elsewhere on the steppe.

It's bizarre and worrying that so many of you want to deny the bleeding obvious. Can you read graphs or not?

http://eurogenes.blogspot.com.au/2015/07/population-genomics-of-early-bronze-age.html

Amanda S said...

@Romulus Polygamy doesn't lead to star like expansions in sub clades, it leads to bottlenecks, as per the Gorilla/Chimpanzee study I read. It's obvious when you do the math. It doesn't matter who is boinking them, 100 women produce 100 * (FERTILITY RATE) children. It can be 1 guy or 1 million guys. The fertility rate is the limiting factor and that is wholly dependent upon subsistence strategy.

Yes, the ability of a society to grow rapidly is limited by the fertility rate of its women. This is why bringing in women from a neighbouring society enables it to grow more quickly than otherwise by capturing their fertility for its benefit. In this situation instead of polygamy leading to a situation where only a few of the men can reproduce, you get one where most of the men can reproduce and with more than one women (dependent of course on the availability of women). This is different than the situation that you describe with gorillas.

I would assume that in the initial formation of the Steppe pastoralist society, you had a mixture of Caucasus farmers and Steppe hunter gatherers but I think we should be cautious of imagining that this mixture initially took the form of hunter gather men and farmer women. It's far more likely that the initial phase involved the attempt of a farmer community to establish itself on land north of the Caucasus. I think that once established its dynamic was such that it sucked in the hunter gatherer men (maybe because of their horse handling skills) differentially from the farmer women.

Romulus said...

The Latvians are Pre-M73 according to Genetiker.

Who's high in M73? Non Indo-European speaking Bashkirs.

You know those Latvian HGs were speaking proto Basque.

Bashkirs & Basques.

Romulus said...

@Amanda S

Doubling the amount of women in your society in one generation is a totally insignificant event compared to the compound interest effect of increasing the fertility rate / subsistence strategy.

@Richard

That's an unfortunate comment, and not a fair assessment of Davidski at all. Genetic study gives us objective facts so that nationalistic bickering can be settled once and for all. It brings people closer together even if the process is painful.

Romulus said...

I think the trend in human bias is to want to ascribe all the success of modern societies to the group of which we are a part of. The truth lies between our individual bias. There are no purebreds left, so it's obvious wherever genetic superiority lies is in a combination of all ancestral European components.

That said the Sardinians are pretty pure and when you contrast them against the Kets or Karitiana they're quite a bit more advanced LOL.

Amanda S said...

Richard, the problem is in thinking that social groups who have been able to expand in history at the expense of their neighbours because they are in possession of some cultural killer apps, to borrow Neill Ferguson's terminology, do so because they are intrinsically superior to their neighbours. This is the fallacy.

Roman armies were very efficient at beating those of their Northern neighbours even though their soldiers are known to be generally smaller because they used superior military tactics and organisation.

Near Eastern farmers were able to expand into Europe, consigning the inhabitants to the margins, to the lands where their farming package was ineffective because farming as a technology massively increases the number of humans that an environment can support. It wasn't because the farmers were intrinsically better human beings than the hunter gatherers of Europe. Than the farmers later themselves came under pressure and appear to have been dominated by this Steppe group because of cultural advantages that they were able to deploy. This happened more in Northern and Central Europe where the existing farming package was less successfully adapted to the environment than in Southern Europe.

Romulus said...

@Amanda S

"Near Eastern farmers were able to expand into Europe, consigning the inhabitants to the margins"

That is factually incorrect.

http://www.academia.edu/1469446/Interaction_between_hunter_-_gatherers_and_farmers_during_the_Neolithic_in_Poland

Amanda S said...

@Romulus

Doubling the amount of women in your society in one generation is a totally insignificant event compared to the compound interest effect of increasing the fertility rate / subsistence strategy.

And why should this have happened in just one generation. The point is that the pastoralists were mobile. They could have returned generation after generation to acquire wives in the North Caucasus. All agricultural societies have the tendency to produce surplus children and this gets to be a problem when there is no new land for them to expand into. Then they face difficult choices as to whether to divide land amongst the offspring into smaller and smaller pieces. The point being that these farmers could sustainably give their 'surplus' daughters to their Steppe neighbours without suffering their own demographic decline.

Rob said...

Amanda
I think the pastoralist exogamy issue is valid but has been overestimated, because most are confused as to when the lineages actually expanded (it occurred much later than the Copper Age. So calculations have been skewed).

Aram said...

Romulus

M73 in Bashkirs is 1100 year old founder effect. The same is true about Mongolian M73.

Amanda S said...

Rob,

I agree that the major expansion occurs later when these people start migrating off the Steppe but the initial stage was transformative of the population on the Steppe itself. It went from being a very lightly populated hinterland to an area with a large and mobile population which was able to threaten and takeover other other settled regions.

Amanda S said...

@Romulus

I use the term "margins" in relation to the efficacy of the Neolithic cultural package. I think that the margins, in Northern Europe especially, must have been very large. There was definitely scope for cooperation as well as conflict between farmers and hunter gatherers. The problem is that when the going gets tough and the crops fail and the animals die, the farmers are back competing with the hunter gatherers for the wild resources.

Ariel said...

Davidisky

That Treemix is irrelevant, obviously CW has direct Yamna-like ancestry, a lot of it, just for the EHG alone. What's the point? Presumably Treemix will also find a similarity beetween CW and the EHG group who moved early in Ukraine, in the baltics, in Scandinavia and in the Balkans. And it will also find similarity with groups that are dead end but that shared some ancestry with them. All those people were similar and thus it's complicated. But my point is simple, CW has EHG, that doesn't mean that ALL the EHG in CW and BB came from Yamna. Some of it did, unquestionably, but for the extra EHG as right now we don't know the source. Your theory is that western Yamna will have more CHG and less EHG. You are choosing to belive that, fine! But they had never been tested. As right now it's only a speculation.

Amanda S said...

Rob, the other key point about the exogamy issue is that it set up a cultural pattern which then shaped the way that settlers from the Steppe interacted with Northern European populations in the Corded Ware culture phase.

Rob said...

Amanda
I certainly agree a package of innovations, including social, were introduced. Still, these formed in those pastoralists closest to farming communities, although it would be a false dichotomy to classify a small such. Communities like Majkop , CT and Baden contained already elements of both
Ultimately, more aDNA will inform of overall pace and dynamics of change

Ric Hern said...

Regarding the building of Monuments etc.and its connection to Farming. As far as I could find is that Gobekli Tepe was not constructed by Farmers. So the building of Temples etc.are not specifically linked to Farming but rather the abundance of food in an area...

Maju said...

@Alberto: can I borrow your spreadsheet to use it for when I write an entry at my blog on this paper? With due attribution of course.

Or, alternatively, if you wish to write a guest entry... I'm always open to intelligent contributions (and I must say that yours is a gem in a very muddy place).

Samuel Andrews said...

@Rob,
"Do you still think I2a2 expanded fr iberia ?"

I never said I2a2 expanded from Iberia, I mentioned a Chalcolithic site from the Basque country had lots of I2a2a. There's also a few from Bronze age Hungary.

Ric Hern said...

Regarding the Romans we see that they incorporated many strategies of War. Fueling feuds between Gallic tribes etc.
It is also not a secret that Romans adopted many desirable objects that other cultures offered. Eg.The Roman Helmet had its origins within the Celtic Warrior Wardrobe etc.
Each culture had his Heyday and each had his Lowday.
We can not look past the fact that some were superior during a specific timeframe within a specific environment.
I think Superior should be interpreted as Having The Edge, that special something extra that other cultures did not have at the specific time and place to be able to excel.
If I own a Ferrari and you own a Volkswagen and I my car is faster than yours, that is a Plain Fact and has got nothing to do with discrimination, favouritism or any other -ism.
So when we find that the Majority of Indo-European speakers today are Haplogroups R1a and R1b it is certainly not discrimination or favouritism when we look at their origins because they central to the issue at hand.

Samuel Andrews said...

I have created a proxy for Ukrain HG/N and Latvian HG in one of David's D-stat spreadsheets based on the EHG/WHG proportions David posted for them earlier.

D-stats do a better job at differentiating EEF, CHG, WHG, EHG than PCA and the ADMIXTURE test Basal rich K7. In those methods EEF absorbs WHG and CHG, CHG absorbs EEF and EHG. D-stats don't have that problem.

Here's a spreadsheet with results using Ukraine HG/N, Latvian HG.
https://docs.google.com/spreadsheets/d/1n1K24L3y6ZpUG6p1VFHurJPcvB-PoQ0HOOd7eWU4Ris/edit#gid=0

Corded Ware Germany scores 20% Ukraine N when modelled with early Neolithic/Mesolithic genomes. But they score only 6% when modeled with Yamnaya Samara and Esperstedt MN. Hungary BA probably has a lot of Ukraine HG-type stuff but we've already known that for a while.

Gioiello said...

How many nonsense! Romulus says "The Latvians are Pre-M73 according to Genetiker. Who's high in M73? Non Indo-European speaking Bashkirs. You know those Latvian HGs were speaking proto Basque. Bashkirs & Basques"
Apart the stupidity of linking Basques and Bashkirs (have you some knowledge of these peoples and languages?), to which Aram correctly answered ("Romulus M73 in Bashkirs is 1100 year old founder effect. The same is true about Mongolian M73)". Have you read (and understood above all) what I wrote in another thread?
"It is clear that all these R-M73 found in Latvia (as the previous found before) are mostly dead end line, because only one of them survived in Eastern Europe/Asia, and, after long bottlenecks, gave life to the R-M73-M478* lines of to-day. Western European samples descend from an R-M73+ (M478-), thus they don't come from these samples. Of course we may not exclude that also the Western European ones descend from one of these R-M73* samples, but that would be against all what we found of the upstream subclades in Western Europe. Of course a deep SNP test on some of these samples will be useful".
And what is demonstrating also this last paper? That R1a and R1b were the haplogroups of the European hunter-gatherers (till yesterday also the kurganists thought to WHG different from EHG and CHG, now that it is clear that they were the same in all Europe, and very likely R1a and R1b came from WHG, they say that they are the same!) We'll see next if my theory of an Italian Refugium will be confirmed: so far I have Villabruna 14000 years ago, and am waitng that an R1a the same old is found somewhere (of course I expect amongst the Villabrunas).
It isn't demostrated that farmers came from Middle East. Many may have come from northern Anatolia and Southern Europe, who were the same WHG descendants.
You spoke of identity. It is a complex issue. Look at Ashkenazic Jews, who are as to the same Davidski 51% Tuscans and other Europeans and only about 30% similar to Samaritans (I think not more than 10%/20%), but I am trying to answer the question if Israel is the consequence of WWII or its cause.

Samuel Andrews said...

(continuation)...

Modern Lithuanians fit as 90% Belrussian+10% LatvianHG. When modeled with Corded Ware Germany, EsperstedtMN they still score about 10% LatvianHG. mtDNA wise 10% Latvian HG makes more sense than the 30% PCA and ADMIXTURE give Balts.

Balts N=442
U5a: 11.3%
U5b: 3.6%
U4: 5.2%
U2e: 2%
Total EuroHG mhg=22.1%

Poles N=840
U5a: 6.2%
U5b: 4.4%
U4: 4%
U2e: 0.8%
Total EuroHG mhg U=15.4%

Dutch N=680
U5a: 5.6%
U5b: 3.4%
U4: 2.6%
U2e: 0.6%
Total EuroHG mhg U=12.2%

90% Polish+10% EuroHG=24% EuroHG mtDNA
Balts have 22% EuroHG mtDNA.

Since there's no documentation of loads of R1b M73, I2, R1a1* in Balts if anything BalticHG was given more by U5a/U4 bearing BalticHG females than R1b M73 bearing BalticHG males.

Balts not having more U5b than other Europeans suggests BalticHGs were mostly U5a, U4, U2e like the MotalaHGs and Russian HGs.

Samuel Andrews said...

I'll be posting interesting stuff about European mtDNA at my blog soon. mtDNA does suggest Steppe-MN admixture was sex bias, hence tiny 6% U5a in Poles+Dutch, 2.5% U5a in Spanish but 15% U5a in Andronovo and 20% in Yamnaya.

Samuel Andrews said...

@Alberto,

I'm starting to think you're right about Srubnaya outlier having ancestry from an unsampled mostly ANE population which roamed Northern Eurasia. HungaryHG has a tiny bit of ANE, UkraineHG has a lot of ANE, SamaraHG has lots more ANE......maybe Central Asian HGs have lots more ANE than SamaraHG. This was hard for me to believe because I assumed the currently ancient genomes could explain everything.

mickeydodds1 said...

Romulus,

Whenever did the Romans 'dominate' the Irish?
Anyhow R1b is very common amongst Italians and Germans - both ancient and modern.

mickeydodds1 said...

Romulus.

You know very little about European history - I'm pretty sure you are not a European.
Ireland 'a thousand years ago' was 'the light in the west' a centre for scholarship and learning. And of course, a thousand years ago Scandinavia was the home of the Vikings, of which I have no need here to proclaim their fame.

Gioiello said...

@ mickeydodds1

There are many Levantines all around who like Arian names like Agamemnon, Alexandros and perhaps also Romulus. They don't know that who will exam their blood am I, and in fact of Y I think having no rival ...

Davidski said...

@Ariel

Your theory is that western Yamna will have more CHG and less EHG. You are choosing to belive that, fine! But they had never been tested. As right now it's only a speculation.

That's not my theory. What I accept is the already published finding that Corded Ware came from an Yamnaya or Yamnaya-related group with slightly inflated hunter-gatherer ancestry relative to Yamnaya Samara.

So these new Baltic samples don't change a thing. In fact, Latvia LN1 totally fits the bill as an unadmixed Corded Ware individual from the proto-Corded Ware homeland somewhere on the steppe.

Alberto said...

@Maju

Yes, sure, you can use that spreadsheet in your post (that will be much better written by you, I'm sure. But thanks anyway). The numbers are calculated from the Global 10 PCA data provided by Davidski.

epoch2013 said...

@Rob

Was that with Loschbour and Yamnaya?

Rob said...

@ epoch

Had loschbour, Hungary HG, and Karelia and Samara HG

Blasonario Cremonese said...

Gioiello wrote:

"There are many Levantines all around who like Arian names like Agamemnon, Alexandros and perhaps also Romulus. They don't know that who will exam their blood am I, and in fact of Y I think having no rival ..."

In fact of good taste and humility you have to work hard, though.

Gioiello said...

@ Blasonario Cremonese

Others use Arian nicknames, you just an Italian one. As to "good taste" I may say that I used my name and surname from the beginning, and also my Y, mt and Full Genome are at disposal of everyone. As to the rest you should know what happened in these last ten years on the genetic questions, who wrote the papers, who funded them, who supported that R1b came from Middle East and after from the kurgans, all against my "Italian Refugium" etc etc. About what happened before, i.e. all in History, I thing having nothing to learn from you or any other. If you desire to know me, you have all my data, but I haven't yours, and amongst us the only one who may be a "lupo solitario" are you.

Maju said...

@Alberto: OK, thanks, I guess I will also have to attribute David then (*grumble-wink*). In any case I think that your qualification (or is it quantification?) of the Latvian and Ukranian samples is quite revealing, particularly because you compare to Motala, which the original paper just ignores. We can now "feel" better the changes that happened in Eastern Europe and something that seems apparent is that: (1) EHG was not present in the Baltic area (nor really increases significantly over there with time, SHG or something similar does instead) and that (2) EHG seems to decrease in Ukraine over time and again Motala increases. That's weird, I would have expected otherwise (migration northwards from Ukraine to Lithuania but anyhow this study does not cover the "core" Kiev area but the less central Odessa coast), but interesting in any case: it shows once again that regional patterns do not adjust quite well or even at all to the simplicity of the "triangular model", that there seems to have been many distinct populations with peculiar "admixture formulas" or "genetic recipes" in all the relevant periods, which we are not going to grasp well enough unless we begin getting extensive geographic coverage of all or most blank areas and cultures; what happened in one region, say Eastern Germany, is not necessarily extrapolable to all the subcontinent, in fact in most cases it does not seem to work well at all.


@David: BTW the steppes do not include Latvia (nor Poland) nor anything nearby, they basically stop existing near Kiev and Bucharest. I'm guessing that you mean the North European plains, which may be related in the broad sense of being "flatlands" (good for horse riding and such) but are not steppe-like in any other way.

Anyway: weren't Corded Ware types (autosomal DNA wise) a simple Yamna (or as someone pointed, probably correctly, that better use Khvalynsk or even Maykop instead) plus lesser local Central European farmer admixture? The only difference seems to be in the Y-DNA (R1a instead of R1b-Volga) and that is way too easily subject to founder effects, be it because they borrowed the lineage from local farmers in the pre-Corded but Kurganish period or because there was a clan-specific founder effect with the Catacombs-derived founder influence in Cuyavia.

BTW, we do not have any Catacomb culture ancient DNA yet, do we? We also do not have any Cuyavian (or otherwise ancient "Polish") farmer DNA, right? We do have some mtDNA but no autosomal nor Y-DNA data I'm aware of. Much like I argue that it's critical to gather data from Atlantic Europe, I'd argue that, if we want to understand the genesis of Corded Ware (which forms in Cuyavia, around modern Warsaw and not anywhere else), we need data from the region (and definitely Latvia is just not close enough for that, nor is East Germany nor Yamna probably either). I know I'm being "demanding" but the real point is to water down the expectations for final answers to the European genesis puzzle until we have extensive aDNA samples, something that to date we only have for mtDNA (if at all).

Maju said...

Erratum: "but anyhow this study does not cover the "core" Kiev area but the less central Odessa coast" should have been deleted before posting (but seems I forgot): it's just wrong, the Ukraine samples are from the Dniepr area SE of Kiev. Sorry. :(

Gioiello said...

I am seeing in old posts that you said enough. If you wanted to be a "lupo solitario", you may not to be that anymore: "I belong to haplogroup G2a3 [...] I'm a genealogist and a Ph.Dr. in Classical Philology". I may find you and also write a book of psychoanalysis about you. Certainly Davidski is a rude Slav ("when you're either an idiot troll or just a complete idiot [...] Are you insane? Do you need psychiatric treatment?"), but not all in Europe are leftists and prone to be invaded, and you know that I fight for an Europe allied with Russia, only because only Russia has the right weapons. About your PhD, taken in this "cattocomunista" Italy, I may fight with you in any matter. Being a phylology, you certainly may understand my last poem. It needs an entire life for writing that:

MAURIZIO FERRARIS
Estetismo un po' pazzoide è d'Annunzio a Fiume?
E la vittoria mutilata, e i grandi criminali
che fanno due guerre mondiali
e la terza in corso per resuscitare voce leggenda o destino
al di là di genetica e verità?
E' il suo un giudizio determinante o riflettente?
Parla di estetica e di uno che ad essa ha dato parole
piene e non libellule di bozzacchione
questo cacamerda dalla pancetta eunucoide,
questo sofo bariccato in tronchi di carciofo.

Davidski said...

@Maju

Ukraine N probably belongs to R1a. Keeping that in mind, have a look at the plots I posted above.

Ukraine N is a low quality sample, so the most sensible thing we can do is to focus on its PCA results in the most significant dimensions. Other dimensions are likely to be skewed IMO.

Now take a look where Corded Ware Latvia LN falls on these plots: almost right between Ukraine N and Caucasus Hunter-Gatherers.

What does that suggest? It suggests that Corded Ware is derived from Ukraine N, in other words, Dnieper Donets, one way or another, after the influx of Caucasus Hunter-Gatherer ancestry into the area. How did Caucasus Hunter-Gatherer ancestry get there? Amanda S explains here...

http://eurogenes.blogspot.com.au/2017/02/first-look-at-baltic-and-ukrainian.html?showComment=1486247659559#c513073137675826373

This doesn't contradict the fact that Corded Ware is very similar to Yamnaya, and that it might even be an Yamnaya offshoot. That's because Yamnaya itself can be modeled as a mixture of Ukraine N, Caucasus HG, and Lengyel LN.

Kalmykia and Samara Yamnaya probably aren't a mixture of Ukraine N, but rather a very similar forager group from around the Don or east of the Don, hence the R1a vs R1b dichotomy between Corded Ware and the Yamnaya sampled to date.

I can also tell you that you shouldn't expect any surprises from Central Poland. Expect Y-HG I, mostly I2, from prior to Corded Ware, and R1a only after Corded Ware. This isn't speculation on my part.

Olympus Mons said...

I've been reading you all, and it like watching David attenborough ... but as if he wasn't ever actually been there! It fits the new world where opinions are facts (alternative).

I still maintain there is a lot of problems here with the concept of space and time. with enough time, every pop was everywhere (sort of). nobody is even close to anything remotely near the "truth".




epoch2013 said...

@Rob

Thanks a lot. The Latvian sample itself looks like a mix between Motala and Loschbour:
https://docs.google.com/spreadsheets/d/12LI5EdWNjpzpxxaSeU_GDj0nTfApnMz9iZJcytmjSWs/edit#gid=0

Rob said...

Epoch
I wouldn't say it's a mix of Motala and loschbour, as they're all just points on a punctuated continuum

Blasonario Cremonese said...

Gioiello said:

"I am seeing in old posts that you said enough. If you wanted to be a "lupo solitario", you may not to be that anymore: "I belong to haplogroup G2a3 [...] I'm a genealogist and a Ph.Dr. in Classical Philology". I may find you and also write a book of psychoanalysis about you. Certainly Davidski is a rude Slav ("when you're either an idiot troll or just a complete idiot [...] Are you insane? Do you need psychiatric treatment?"), but not all in Europe are leftists and prone to be invaded, and you know that I fight for an Europe allied with Russia, only because only Russia has the right weapons. About your PhD, taken in this "cattocomunista" Italy, I may fight with you in any matter. Being a phylology, you certainly may understand my last poem. It needs an entire life for writing that:

MAURIZIO FERRARIS
Estetismo un po' pazzoide è d'Annunzio a Fiume?
E la vittoria mutilata, e i grandi criminali
che fanno due guerre mondiali
e la terza in corso per resuscitare voce leggenda o destino
al di là di genetica e verità?
E' il suo un giudizio determinante o riflettente?
Parla di estetica e di uno che ad essa ha dato parole
piene e non libellule di bozzacchione
questo cacamerda dalla pancetta eunucoide,
questo sofo bariccato in tronchi di carciofo."

Well, my name is the title of the project I made: the Blasonario Cremonese online... if you want, you can pay a visit to my site, just search on the net typing Blasonario Cremonese. I chose that name because I want to advertise my site.

I said enough, yes... and you also: I took a phD in Italy and, like you, I know that the games are done here. Only with Saints in Paradise or, better, with a teacher that can help you with selections you can reach my results. I am aware of this... no problem with me. I only want to say that I could make my way in the PhD not because of my links with academic environment, nor because of my good education, but because I managed to choose the right moment, when there was a change in the head of PhD and when all the cadidates from that university where already chosen. Ok, buy me a psychoanalysis book... I will read it with interest... but I suggest you also to buy one: I am the only open to all possibilities here about Y-DNA origins. If you read well, you would recognize that I went against Davidski only in general assumptions, because I felt that we would have waited for some time in order to know better the situation. It is easy to make assumptions when you have an agenda. Now, I only favour an eastern origin for R1b, but not because of a sort of steppic pride, but only because I stick with the data.

Ok, understood your poem... but the main problem remains: I think you are too much obsessed by conspiracies against your person. I know that we live in a cattocomunista Italy, with the, as I call it, "pateticamente corretto" ruling over our lives... but what will we do? Did you see that those so-called "reati d'opinione" are more persecuted than, for example, murders or other?

Dmytro said...

"you shouldn't expect any surprises from Central Poland. Expect Y-HG I, mostly I2, from prior to Corded Ware"---(David) So that is where I2a1b of the L621 variety etc.. was "hiding" up to the 4th mill. BCE? And in Funnelbeaker and GAC? That would seem very plausible. So far the only aDNA available as to "ancestors" is from Luxemburg and Sweden.

Gioiello said...

Oh, yes, you are an open minded person, and Davidski has been and is rude with everyone, with me too, above all before Villabruna, now perhaps he is more prudent, but the blog is his and we have to be glad of being published. About the origin of R1b from East I'd be more prudent than you. I wrote more than 10000 letters about that, in my bad English, and so far I think that nothing happened to disprove my theories, neither these massive R-M73* (whose only one sample survived in Eastern Europe/Asia and another in Western Europe: Italy has 2 +1 samples known so far). Read what I wrote recently about R-V88...

Maju said...

@David: I can't comment, I've tried twice and get "bad request" errors after captcha verification, so I'm giving up. Suffice to say that, unsurprisingly, I disagree.

Matt said...

Another nMonte experiment with the Days of High Adventure PCA.
Calc pops (used for ancestry):

Mesolithic HG from across Europe - Iberia_Mesolithic, Loschbour, Latvia_HG and Ukraine_N1

Neolithic influx - Boncuklu, Kotias

Test Pops: Modern Europeans - Albania, Austrian, Basque_French, Bulgarian, Czech, Dutch, English_Cornwall, French, German, Greek, Greek_Peloponnese, Hungarian, Irish, Italian_North, Italian_South, Lithuanian, Norwegian, Polish, Russian_West, Sardinian, Scottish, Serbian, Spanish, Swedish, Ukrainian West

Results: Sorted by different types of HG ancestry - http://i.imgur.com/QLMy73S.png, Sorted by Boncuklu level - http://i.imgur.com/qmg5JuO.png, Sorted by Kotias level - http://i.imgur.com/koVj0ha.png

Results PCA (1v2): http://i.imgur.com/7IG175A.png, Results MDS: http://i.imgur.com/eWmmpTA.png, Neighbour Joining Tree: http://i.imgur.com/XWOYDyt.png

So, strange results. On the one hand, they are fairly systematic with the modern day European substructure...They would've fit with one of the old models we had from years ago, with a wave of advance of farmer ancestry, followed by absorption of local HGs with more in north and less in south... (Along with an odd peak of Kotias ancestry in Scotland and Ireland for some reason, declining out of there with distance).

But on the other don't really fit at all well with our current models, where we know that there was discontinuity in each region and relatively sudden increases of steppe related ancestry, and this is shown by f4 and D-stats.

I think I'm going to try merging the datasheet for Days of High Adventure PCA and Globe10 PCA, and then re-run this exercise. I think there's probably some information in the global relationships (best caught by Globe10) that can add to the local ancient relationships (best caught by Days of High Adventure) that could refine.

(Lots of strange comments here yesterday... :| Even more so than normal for some people)

Blasonario Cremonese said...

Gioiello wrote:

"Oh, yes, you are an open minded person, and Davidski has been and is rude with everyone, with me too, above all before Villabruna, now perhaps he is more prudent, but the blog is his and we have to be glad of being published. About the origin of R1b from East I'd be more prudent than you. I wrote more than 10000 letters about that, in my bad English, and so far I think that nothing happened to disprove my theories, neither these massive R-M73* (whose only one sample survived in Eastern Europe/Asia and another in Western Europe: Italy has 2 +1 samples known so far). Read what I wrote recently about R-V88..."

I am, partially, at your side when you are talking about the Italian refugium and the possibility of an origin of R1b and - as you state - also R1a in Italy. For sure, I always thought that, probably, at least R1b-V88 was born in Italy and, from there, it spread in the Mediterranean and in Africa. But, if I may, I only want to know how do you concile the origin of R1b in Italy and the formation of the culture from the Paleolithic to the Iron age and, of course, their ethno-linguistic affiliation. For example, if R1b was born in Italy, with also - as I seem to understand from what you write - also some of its sublcades, like L51... so, what language did they speak? What culture did they brought? It seems that they were borrower of culture, more than creator!

John Smith said...

@ Richard Holtman

"What the hell is wrong with being in Haplogroup G2a?"

Nothing is wrong with it. On this blog, you have a few types of people:

1) The crazy Italians who think every lineage of Europe somehow hid in Italy during the LGM before spreading and taking over Europe. Italy's accomplishments in the Roman era aren't enough for them -- no, they want to claim the neolithic and the metal ages too.

2) The crazy Poles like Davidski himself who believe that Europe was built on R1a (lol). Or those who overestimate the importance of the IE's in general. Yes, the IE's were important (especially linguistically), but there was a lot going on in Europe prior to them.

3) Indian nationalists. They are the guys who don't believe in the Aryan Invasion Theory of the Indus Valley and think it is some colonialist conspiracy invented by the British to keep the brown people oppressed. They are the same people who believe the PIE language originated in India (along with R1a and R1b). Indeed all the evidence (historical, linguistic, archaeological and genetic) point to this "Out of India" hypothesis as being complete bunk.

4) Generalized white nationalist types. They don't care what haplogroup did what -- as long as there isn't any damn Asian or SSA DNA mixed in there (OK a little East Asian ain't no big deal, but definitely no SSA). These are also the guys that still can't let the "Kennewick man was white" myth go.

5) The more serious scientific types like Rob, Sam Andrews, Alberto and others who don't appear to have any obvious bias toward any group.

6) People like me who are not experts, but find the topic fascinating anyway. Getting a chuckle out of all the nationalists is just icing on the cake.

Gioiello said...

@ Blasonario Cremonese
"I am, partially, at your side when you are talking about the Italian refugium and the possibility of an origin of R1b and - as you state - also R1a in Italy. For sure, I always thought that, probably, at least R1b-V88 was born in Italy and, from there, it spread in the Mediterranean and in Africa. But, if I may, I only want to know how do you concile the origin of R1b in Italy and the formation of the culture from the Paleolithic to the Iron age and, of course, their ethno-linguistic affiliation. For example, if R1b was born in Italy, with also - as I seem to understand from what you write - also some of its sublcades, like L51... so, what language did they speak? What culture did they brought? It seems that they were borrower of culture, more than creator!"
Unfortunately you didn't read me a lot in the past because I have written about all what you ask me in the past and wouldn't want to abuse of the patience of Davidski here. The R-L51 map (which peaks in Italy and was done from Argiedude and me many yeras ago) is my avatar, in fact the kurganists haven't found any R-L51 in the Eastern European kurgans and are hopping in the western part: let's wait and see. Of course I think that hg. R came from the Siberian corridor and that the R1b1 found in India, but coming from central Asia, hadn't anything to do with us, I said first probably and made Raza and Joshi test, in fact they are L389-. Search my posts and read: I am not only Gioiello, but also Maliclavelli, Rathna, Claire (the name of the daughter of Vernade when DNA-forums banned me). No confusion: my names belong only to the masculine gender.

Blasonario Cremonese said...

@ John Smith

You forget another cathegory: the Iberianists and Basque nationalists.

Gioiello said...

@ John Smith

Ahahaha, you are funny, and in many things I agree with you. About me and my Italian Refugium perhaps you ignore that R1b1 (probably at the P297 level, having two mutations at that level) has been found at Villabruna (14000 years ago). I posted about infinite other haplogroups, both Y and mt, which are older in Italy than elsewhere, and of course I am waiting that they are found in the aDNA for proving or disproving my hypiotheses. The last the mt X2 (HVR2: 73G 153G 225A 263G
CR: 750G 1438G 1719A 1888A 2706G 4769G 6221C 6371T 7028T 8860G 9449T 11719A 12705T 13966G 14470C 14766T
HVR1: 16092C 16278T (16519C) and tested only partially from 23andMe that Marco Grassi sent me yesterday . I have tons of them.
About Samuel Andrews (alias Krefter, Sammy etc etc) I may send you tons of his letters as a Jewish integralist who, if he could, would pull his European ancestry up, and it risks to be till the 80%. He is also mt K1a1b1a and I am K1a1b1e, certainly born in Tuscany.

a said...

Blogger Blasonario Cremonese said...

@ John Smith

You forget another cathegory: the Iberianists and Basque nationalists.



Or the Ethiopian nationalists.

Blasonario Cremonese said...

@ a

Never seen an Ethiopian nationalist...

I have Ethiopian citizenship, and, perhaps, I'm the only ethnic Italian livign in Ethiopia discussing about genetics on the web but I'm interested only in European genetics, because I come from there and I am fully Italian.

a said...

Blasonario Cremonese said...

@ a

Never seen an Ethiopian nationalist...

I have Ethiopian citizenship, and, perhaps, I'm the only ethnic Italian livign in Ethiopia discussing about genetics on the web but I'm interested only in European genetics, because I come from there and I am fully Italian.


I'm fortunate to have met many people of various backgrounds[Italian,Ethiopian etc...]male/female/other. You would be surprised, some of the most vocal people singling out others and preaching social justice and an end to intolerance[pointing the finger primarily at white males], are often very prejudice themselves.
It's almost as if they are under the impression that when they leave the toilet stall, it smells like fresh cut roses.
Just a personal observation,everyone smells bad.

At the end of the day, many are at this site want to find out about their ancestors; nothing more nothing less[it is called Eurogenes after all]. The dialect we communicate is a Indo-European based West Germanic language, that has it's roots in a patriarchal clan system. Something not many people are even interested in when you try and discuss the subject.
Hopefully when then next batch of samples/reports arrive many of us will have some closure to our ancestry/lineage questions.


Grey said...

@Richard Holtman

"What the hell is wrong with being in Haplogroup G2a? I'm in Haplogroup G2a and I'm proud of my farmer ancestry."

It's different personality types imo - some people prefer the idea of their ancestors being the civilized farmer types and some prefer the more macho tattooed biker gang thing.

Grey said...

Amanda S

" It's far more likely that the initial phase involved the attempt of a farmer community to establish itself on land north of the Caucasus."

I think that makes most sense as the general pattern - farmers expanding to the edge of viability and if there's land beyond that point acting as a catalyst for the formation of a pastoralist culture on the other side of the line which often *eventually* gets strong enough to destroy them.

With the "eventually" part often being a long time.

epoch2013 said...

@a

"At the end of the day, many are at this site want to find out about their ancestors; nothing more nothing less"

I don't know my Haplogroups. I am interested in this because DNA because it gives an unprecedented possibility to calibrate and double check archaeological theories.

Back in the days I read my first popular science books most archaeological disputes were considered unsolvable. This trip that paleoDNA is, is an unbelievable gift.

Grey said...

Maju

"BTW the steppes do not include Latvia (nor Poland) nor anything nearby, they basically stop existing near Kiev and Bucharest. I'm guessing that you mean the North European plains, which may be related in the broad sense of being "flatlands" (good for horse riding and such) but are not steppe-like in any other way."

quibbling a bit as the north european plain used to be part of the steppe at one time before it shrunk as the world warmed up after the ice age. reason for quibbling is what if that shrinking is somehow the connection between Villabruna and Yamnaya?

Maju said...

@Grey: the North European plains used to be under a massive ice sheet, that's part of the reason why they are so flat. Nobody lived in Poland, for instance, before the Holocene... unless it's Neanderthals before the last glaciation. There used to be a steppe-tundra (not exactly like modern steppe) ecosystem that was present in many parts now more temperate of Europe, for example the Rhine-Danube region, some sources call it "the mammoth steppe" and maybe that's what is confusing you. Anyway, everything under discussion here is within Holocene time-frame and therefore climatic conditions similar to present ones, so never mind "the mammoth steppe" (steppe-tundra).

Davidski said...

@Maju

Which part do you disagree with? There's really not much space for debate in what I said considering all the data we have now. My guess is that you're not aware of the data or you don't understand it.

And why do you keep complaining about the word verification? Just tick the box and move on.

capra internetensis said...

@Davidski

I know what Maju is talking about- the page crashes with "Bad Gateway" message, and you have to reload the page and lose your work. It happened twice before this message would post, in fact.

@Grey

It's not like the farmers were exactly peaceable folks themselves. I think people project back a lot of stereotypes that have nothing to do with reality.

The example of an *actual* matrilineal Neolithic farmer society that first comes to mind is the Iroquois. Yeah, real fluffy pushovers those guys.

capra internetensis said...

Sorry, it is "Bad Request - Error 400"

Annie Mouse said...

@John Smith

LOL. I wonder which one I am. You need a lurker category also I think.

And one for those who think anyone who disagrees with their particular point of view is a racist/nationalist/non-expert. But perhaps the latter come from all of those groups.

Without all these diverse views we would have religion, not scientific debate. Vive la difference.

Roy King said...

@Grey
"It's different personality types imo - some people prefer the idea of their ancestors being the civilized farmer types and some prefer the more macho tattooed biker gang thing."

I find the whole project of identifying oneself with possible actions of remote ancestors to be very strange, indeed! With ancestry from all over the world, I take a more cosmopolitan stance and judge a person or myself through their or my actions. Many here who read and comment on Eurogenes are purely interested in discussing the scientific results and how they impact or modify received archaeological and linguistic opinion. Not an emotional or personal perspective IMO.

Davidski said...

We're about to get to 200 posts, which will make it difficult for people with mobiles to comment, so let's move things to the new thread.

http://eurogenes.blogspot.com.au/2017/02/women-on-move.html

Grey said...

capra

"I think people project back a lot of stereotypes that have nothing to do with reality."

Roy King

"Not an emotional or personal perspective IMO."

different strokes for different folks

Maju said...

@David I'll try to reply now in the new suggested thread. I'm using a separate text file to prevent bad gateway errors from deleting my work a third time.

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