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Friday, December 20, 2019

A note on Steppe Maykop


I'm reading a new book titled Dispersals and Diversification: Linguistic and Archaeological Perspectives on the Early Stages of Indo-European (see here). One of the chapters is authored by archeologist David Anthony, in which he makes the following claims:

A previously unknown genetic population actually was identified in Wang et al. (2019), but it was a peculiar relict-seeming group related to Paleo Siberians and American Indians (Kennewick) that had survived isolated somewhere in the Caspian steppes or perhaps in the North Caucasus Mountains. The Maykop people did admix with this previously isolated Siberian/Kennewick population in graves labeled "Steppe Maykop" in Wang et al. (2019).

But this just makes it clearer that a cultural choice motivated the Maykop people to exclude marriages with Yamnaya and pre-Yamnaya people specifically, even while exchanges of material goods, ideas, technologies continued. Neither the Maykop nor the North Caucasus/Siberian/Kennewick population can be the source of most of the CHG [Caucasus hunter-gatherer] ancestry in Yamnaya. In order to narrow down when and where CHG ancestry entered the steppes, we must widen our geographic frame beyond the Caucasus.

Unfortunately, this is way off the mark. Especially unsound is his inference that the CHG-related ancestry in the Yamnaya population may have come from beyond the Caucasus.

In fact, the chances that the Steppe Maykop people were derived from a relict Siberian/Kennewick-related group that survived into the Maykop era in the Caspian steppes or the North Caucasus are exactly zero.

The real story was surely more complicated. In my opinion, it initially involved the migration during the Eneolithic or earlier of a people rich in CHG ancestry from the southernmost steppes into the Volga Delta and surrounds, and then the back-migration during the Early Bronze Age (EBA) of their descendants with around 50% admixture from Central Asian foragers. If so, these foragers were very similar to indigenous West Siberians and also relatively closely related to Native Americans.


I don't know why such an exotic people migrated into the North Caucasus steppes to form the bulk of the Steppe Maykop population, but I'm certain they did, and one interesting possibility is that they were recruited by Maykop chiefs to create a buffer zone against hostile Yamnaya-related groups trying to push into the Caucasus, possibly from the lower Don region.

Of course, the same ancient northward migration of the CHG-rich population that may have eventually given rise to the Steppe Maykop people might also explain the deep origins of the Yamnaya people.

The key sample in all of this is VJ1001 from the Wang et al. paper. This female comes from an Eneolithic (4332-4238 calBCE) kurgan burial in the North Caucasus steppes. But despite her early date, she's genetically very similar to most Yamnaya individuals. And she's also a perfect proxy for half of the ancestry of three out of the six Steppe Maykop individuals. Here's a mixture model that I put together using the Broad MIT/Harvard software qpAdm:

RUS_Steppe_Maykop (3/6)
RUS_Eneolithic_steppe_VJ1001 0.452±0.023
RUS_Tyumen_HG 0.548±0.023
chisq 7.494
tail prob 0.874914
Full output

Indeed, these Steppe Maykop samples don't harbor any Maykop ancestry. They're simply a two-way mixture between a population closely resembling VJ1001 and another one similar to hunter-gatherers from Tyumen, West Siberia.

Importantly, a couple of Steppe Maykop-related populations were inadvertently discovered by Narasimhan et al. northeast of the Caspian Sea in what is now Kazakhstan. One of these groups is labeled Kumsay_EBA, after the location of its cemetery. It's roughly contemporaneous with Steppe Maykop and basically identical to the aforementioned Steppe Maykop trio.

KAZ_Kumsay_EBA
RUS_Eneolithic_steppe_VJ1001 0.440±0.022
RUS_Tyumen_HG 0.560±0.022
chisq 10.573
tail prob 0.646513
Full output

I suppose it's possible that Kumsay_EBA represents the migration of Steppe Maykop people into the Kazakh steppes. But even if this is true, then there had to have been an earlier migration of a group from the Kazakh steppes or West Siberia that mixed with the VJ1001-related natives of the North Caucasus steppes to give rise to Steppe Maykop.

I'm assuming that the Yamnaya-like VJ1001 and her people were the indigenous population of the North Caucasus steppes because there are no indications that they or their ancestors migrated there within any reasonable time frame from anywhere else, and certainly not from as far afield as, say, what is now Iran.

The other three Steppe Maykop individuals, who are genetic outliers in varying degrees from the main Steppe Makyop cluster, show variable levels of Maykop ancestry, with an average of about 50%. But they too harbor significant VJ1001-related ancestry. So despite the fact that there was some irregular mixing between the Maykop and Steppe Maykop peoples, this is not what created the typical Steppe Maykop genetic profile.

RUS_Steppe_Maykop_o
RUS_Eneolithic_steppe_VJ1001 0.234±0.074
RUS_Maykop_Novosvobodnaya 0.461±0.046
RUS_Tyumen_HG 0.305±0.033

chisq 7.378
tail prob 0.831667
Full output

And, of course, it should be obvious by now that the ancestry of the vast majority of Yamnaya individuals is better modeled without any input whatsoever from the Maykop or Steppe Maykop samples.

In fact, early indications are that the Yamnaya people flooded into Steppe Maykop territory from the north and completely replaced its population (see here). Despite this, in Dispersals and Diversification archeologist Kristian Kristiansen makes the following claim: "steppe Maykop expanded north, leading to the formation of the Yamnaya Culture and Proto-Indo-European". Not a chance in hell Professor.

See also...

A final note for the year

The PIE homeland controversy: August 2019 status report

Some myths die hard

An exceptional burial indeed, but not that of an Indo-European

260 comments:

«Oldest   ‹Older   201 – 260 of 260
Aram said...

Rob

The NWC G2 is G2a2b-P303>U1>L1266.
We have P303 from Europe but none of them is positive for U1. We don't have U1 from Caucasus Near East also. The only U1 we have is from a Kipchak burial in Altay. But is too late to give a clue about it's migration.

Archi

I also was believing that those Mycenean are not the true one. But now we have Greeks from Empirus2. They are not different. And there is also Colegno trio who also possibly had Greek origin. While the Crete Armenoi type remains an exception.

Aram said...

Archi

Believe me. Barcin is a practically dead thing there. The J2 in Anatolia MLBA is M67 unrelated to that J2 in Barcin. The G2a2b is M406 which has nothing to do with Barcin European G2a2b. It is a post neolitic expansion. You can find a map of M406 in Eupedia and see Yourself.
Also there are autosomes. That I2c2 from Lchashen do not give impression that he recently came from Anatolia. Notice it's age is 1200 BC. And no evidence that he came recently.

vAsiSTha said...

Davidski said "@vAsiSTha

It looks like your outgroups are garbage."

But im using the same 14 right pops as Wang 2019, you are not. You should inform Wang that his paper is garbage.

heres the EEHG+CHG model for Steppe eneolithic (in the nested result) using Wang's 14 right pops. model is a fail. output link below
result

heres Khvalynsk + CHG (in he nested results) using's Wang's 14 right pops. Khvalynsk + Parkhai is a better model than Khvalysnk + CHG. Parkhai model has smaller chisq and higher tail, although p-values of both are above 0.05 threshold. output link below
result

Need more resolution in the iran component, hence split CHG and put kotias in left, satsurblia in right (so 15 right pops). Dstat also shows that steppe eneolithic shares more allelles with Kotias than Satsurblia for obvious reasons. Here, any 2 way model is a fail and Khvalysnk + Kotias + Parkhai_EN is accepted with p-value 0.84. output link below.
Result

you should also post a good model from your side which works for Steppe_Eneolithic

Davidski said...

@vAsiSTha

Those outgroups are obviously garbage, even though they're from a paper, because a different set of outgroups shows that they don't do the job right.

You can't get around that fact no matter what.

And there are no good models for Eneolithic_steppe, either because the right ancient populations haven't been sampled yet, or, like I just said, Eneolithic_steppe isn't really a mixed population.

EastPole said...

А. Клёсов has published some maps recently on which the routes of ancient R1a and R1b migrations are reflected. He noticed that it all changing all the time:

“I did not favor such cards, because they are constantly out of date. New and new data is progressively appearing, migration routes are being supplemented and revised, and for me they are constantly on the move.”

Here is his R1a map:

http://pereformat.ru/wp-content/uploads/2019/10/R1a-map-2019-1.jpg

http://pereformat.ru/2019/10/r1a-map/


And R1b map:

http://pereformat.ru/wp-content/uploads/2019/11/R1b-map-2019.jpg

http://pereformat.ru/2019/11/r1b-map/

We don’t have to agree with him in everything but it may be some food for thought and discussion. Nothing is proven yet. Carlos doesn’t like Klyosov, and we don’t like Carlos etc….

Anonymous said...

@Aram
"I also was believing that those Mycenean are not the true one. But now we have Greeks from Empirus2. They are not different. And there is also Colegno trio who also possibly had Greek origin. While the Crete Armenoi type remains an exception."

It doesn't say anything. Even in the time of Herodotus, the Greeks were not a single people, they were many different peoples that were different from each other. Empirus is a derivative from a derivative, a colony from colony from the one area, it is not representative of the Greeks, it can be mixed with two local populations and its resemblance to someone can be an accident. The Crete Armenoi is exactly the Achaean indicator, there's no doubt about it. This is the daughter of she Achaean and the local Minoan king.

Bronze Mycenaean period / Late Minoan Greece Armenoi, Crete [Armenoi 503 / I9123] 1370-1340 BC F U5a1
Bronze Mycenaen Greece Grave Circle B, Mycenae [Z59] 1500 BC U5a1/U5a1a

"Believe me."

I believe only in the facts that there is no fact that I2c2 is not of Anatolian origin, just as there is no fact of total extinction of the Anatolian population in Neolithic. There are none, and I will not believe your claims. I'll write to you too - believe me, I2c2 from Anatolia.


Richard Rocca said...

@EastPole,

His R1b is more like food for garbage than food for thought. His now infamous R1b through North Africa through Spain and then to the rest of Europe has already been resoundingly disproved by ancient DNA.

Ric Hern said...

@ EastPole

That R1b spread map is certainly not worth discussing. Just for interests sake, why did you even post it ? Are you trying to disconnect R1b from Indo-Europeans and elevate R1a for some or other reason ?

Ric Hern said...

I personally look at it this way: Most Linguists as far as my knowledge stretches postulate that PIE formed around 3500 to 4000 BCE. R1a and R1b already had interaction before these dates. So why try and elevate the one above the other ?

EastPole said...

@Ric Hern

“Just for interests sake, why did you even post it ?”

I don’t have very strong opinions about PIE homeland. Many things are still possible.
But I love this blog very much and feel that sooner or later we will get closer to the truth, closer than anyone else.
I also want this blog to thrive. This requires new data, new people and new ideas presented in an interesting way. As a consumer I also feel obliged to contribute something from time to time. But there is not much to contribute right now. Not many new important discoveries. Everything seems to be hanging in limbo, just waiting for final resolution. So my dilemma is should I contribute something controversial or nothing. I decided for a controversial thing to avoid boredom. I am not Klesov follower. There are some interesting knowledgeable people here but they avoid making clear statements and present their theories in an interesting and transparent way. So there is a danger of boredom for many readers.

Ric Hern said...

@ EastPole

True.

Ric Hern said...

@ EastPole

All I wanted for Christmas was an R1b L51. Heheheeh.

Anonymous said...

@ EastPole

Klyosov, like Quiles, has no supporters in the scientific world, absolutely no one agrees with them. Even his only supporter Rozhansky left Klyosov, making sure that his constructions were wrong. They write propaganda for feeble brain people who do not understand. All the crazy mistakes nothing to discuss.

Chad said...

Matt,

I was referring to Anatolia HG and not Barcin. They do have Iranian and Natufian ancestry. Their f4 uses Mbuti as an outgroup, which is a problem. Africans are significantly closer Anatolians and later Levantines, along with Iberomaurusians. Chimp is more neutral here. The stats with Africans are even more significant, the older the comparing pop is. It's basically looking like an illusion. I've already talked to Harvard about this, but waiting on a reply. QpGraph requires no Basal Eurasian to Pinarbasi. I can get Boncuklu in there with none too.

Modern East Asians cause an issue too, being significantly closer to Ust Ishim than ancient East Asians and Americans. You can't combine Africans or modern East Asians in analysis.

Richard Rocca said...

@EastPole said "...This requires new data, new people and new ideas".

Problem is, that map was created by someone who has been posting for over a decade using STR variance from modern samples. So, old data, old people and old ideas.

Leron said...

Those 2 maps are an abomination and it reeks of “40 days wandering the wilderness” kind of thinking.

Chad said...

Here's the graph to show that there is no need for BE in Anatolia_HG or Boncuklu. I could add another edge from Tianyuan to Iran, but that isn't terribly relevant here.

https://drive.google.com/file/d/1VPcRLQRsJ02pqqKfUl3mC5TFY--MV0DY/view?usp=sharing

Vladimir said...

Chad. Could you explain in a few words what we are talking about? Are the letters Y-haplogroups or symbols?

Chad said...

Labels for the nodes.

Chad said...

https://populationgenomics.blog/2019/12/30/is-there-really-basal-eurasian-and-or-iranian-caucasus-related-ancestry-in-anatolias-first-hunters-and-farmers-maybe-not/

Davidski said...

@Chad

I'm glad you were somewhat cautious with this and said maybe not, because chances are slim that it'll work out for you.

The thing to keep in mind is that Pinarbasi_HG behaves in very specific ways in a wide range of analyses, and, indeed, expected ways for an individual with a significant cut of the so called Basal Eurasian ancestry.

That is, no matter what Basal Eurasian really is, the broad picture clearly shows that Pinarbasi_HG has more of it than European foragers and only a little less than Anatolian farmers.

There's no way around this fact. So you must be misinterpreting your data in some way. And I'll be flabbergasted if the guys at Harvard get back to you and say that you might be onto something.

Chad said...

Which specific ways, David?

Matt said...

@Chad, so can you get Barcin, Natufian, Levant N, Villabruna and ideally Iron Gates on the same graph? I guess if the contention is that Natufian and Iran N input into Anatolia HG base is sufficient to cover Barcin's Basal ancestry and it's affinity to Villabruna and Iron Gates, then that's pretty important.

The graph seems somewhat complex in that you have very many 0 / 1 / 3 drift edges.

Davidski said...

@Chad

Pinarbasi_HG sits more or less in the middle of a cline that runs from the supposedly least basal to the most basal West Eurasian populations, and this cline can be reproduced using a wide variety of methods, including PCA, formal stats, IBS, model based admixture, Fst, etc...

Chad said...

PCA means little though. Native Americans get their own pole as a mix too. Which formal stats? If you don't use Africans or modern East Asians those are gone.

Chad said...

Here are some of those stats. Now, you can pick out Goyet, Magdalenians, Yana and Meso Euros getting some affinity to Ust-Ishim. Now, this is not shared with ancient East Asians to that extent, nor Native Americans. So, it could be actually Ust-Ishim admixture into Yana, Goyet, and via them into Magdalenians and Meso Euros. This, I think is more straight forward than having to put Basal Eurasian in all kinds of other groups where it makes less sense.

I do in fact have graphs that show Yana and Goyet receiving admixture from Tianyuan and Ust-Ishim and Magdalenian into Meso Euros. There is an affinity to Goyet that is needed, that is not shared with Anatolia_HG or ANE. Something on the order of around 10-15% Magdalenian into Villabruna, and even more into Loschbour, LaBrana, and the like.

Chad said...

Chimp Ust_Ishim Anatolia_HG Boncuklu_N -0.000343 -0.722 831117
Chimp Ust_Ishim Anatolia_HG Iron_Gates 0.001032 2.16 852301
Chimp Ust_Ishim Anatolia_HG Villabruna 0.00158 2.47 714348
Chimp Ust_Ishim Anatolia_HG SunghirIV -0.000044 -0.062 845798
Chimp Ust_Ishim Anatolia_HG Vestonice_all 0.001162 1.761 625281
Chimp Ust_Ishim Anatolia_HG I-III_Sunghir 0.000959 1.566 852919
Chimp Ust_Ishim Anatolia_HG Tianyuan 0.000646 0.813 683822
Chimp Ust_Ishim Anatolia_HG Vanuatu_2900BP 0.000289 0.411 393449
Chimp Ust_Ishim Anatolia_HG Vietnam_N 0.000315 0.423 312229
Chimp Ust_Ishim Anatolia_HG Goyet 0.00273 3.549 628021
Chimp Ust_Ishim Anatolia_HG ElMiron 0.001917 2.735 522006
Chimp Ust_Ishim Anatolia_HG Magdalenian 0.002308 2.723 163148
Chimp Ust_Ishim Anatolia_HG Yana 0.001391 2.223 853104
Chimp Ust_Ishim Anatolia_HG Brazil_LapaDoSanto_9600BP 0.000812 1.371 766921
Chimp Ust_Ishim SunghirIV Goyet 0.002626 3.37 724721
Chimp Ust_Ishim SunghirIV Magdalenian 0.002369 2.692 184639
Chimp Ust_Ishim SunghirIV Vestonice_all 0.001065 1.542 723907
Chimp Ust_Ishim SunghirIV Yana 0.001597 2.402 1088950
Chimp Ust_Ishim SunghirIV Brazil_LapaDoSanto_9600BP 0.001095 1.656 911512
Chimp Ust_Ishim Goyet Brazil_LapaDoSanto_9600BP -0.001574 -2.174 687545
Chimp Ust_Ishim Yana Brazil_LapaDoSanto_9600BP -0.000432 -0.826 919456
Denisovan Ust_Ishim Anatolia_HG Boncuklu_N -0.000284 -0.6 867058
Denisovan Ust_Ishim Anatolia_HG Iron_Gates 0.000992 2.026 889108
Denisovan Ust_Ishim Anatolia_HG Villabruna 0.001568 2.356 745028
Denisovan Ust_Ishim Anatolia_HG SunghirIV -0.000204 -0.273 882265
Denisovan Ust_Ishim Anatolia_HG Vestonice_all 0.000766 1.1 651926
Denisovan Ust_Ishim Anatolia_HG I-III_Sunghir 0.00091 1.445 889751
Denisovan Ust_Ishim Anatolia_HG Tianyuan 0.001042 1.276 710836
Denisovan Ust_Ishim Anatolia_HG Vanuatu_2900BP 0.000579 0.783 411916
Denisovan Ust_Ishim Anatolia_HG Vietnam_N 0.000274 0.364 326813
Denisovan Ust_Ishim Anatolia_HG Goyet 0.002008 2.488 656019
Denisovan Ust_Ishim Anatolia_HG ElMiron 0.001764 2.444 544306
Denisovan Ust_Ishim Anatolia_HG Magdalenian 0.001587 1.879 170041
Denisovan Ust_Ishim Anatolia_HG Yana 0.00168 2.542 889955
Denisovan Ust_Ishim Anatolia_HG Brazil_LapaDoSanto_9600BP 0.000911 1.452 800215
Denisovan Ust_Ishim SunghirIV Goyet 0.002252 2.775 756470
Denisovan Ust_Ishim SunghirIV Magdalenian 0.001574 1.855 192352
Denisovan Ust_Ishim SunghirIV Vestonice_all 0.001088 1.537 754144
Denisovan Ust_Ishim SunghirIV Yana 0.001959 2.833 1135036
Denisovan Ust_Ishim SunghirIV Brazil_LapaDoSanto_9600BP 0.001207 1.766 950345
Denisovan Ust_Ishim Goyet Brazil_LapaDoSanto_9600BP -0.000904 -1.175 717752
Denisovan Ust_Ishim Yana Brazil_LapaDoSanto_9600BP -0.000622 -1.134 958723
Altai Ust_Ishim Anatolia_HG Iron_Gates 0.000789 1.534 889313
Altai Ust_Ishim Anatolia_HG Villabruna 0.001157 1.671 745174
Altai Ust_Ishim Anatolia_HG SunghirIV -0.000478 -0.617 882442
Altai Ust_Ishim Anatolia_HG Vestonice_all 0.000547 0.756 652059
Altai Ust_Ishim Anatolia_HG I-III_Sunghir 0.000869 1.325 889928
Altai Ust_Ishim Anatolia_HG Tianyuan 0.000457 0.514 710950
Altai Ust_Ishim Anatolia_HG Vanuatu_2900BP 0.000629 0.819 412028
Altai Ust_Ishim Anatolia_HG Vietnam_N 0.00087 1.092 326875
Altai Ust_Ishim Anatolia_HG Goyet 0.001589 1.822 656145
Altai Ust_Ishim Anatolia_HG ElMiron 0.00108 1.427 544405
Altai Ust_Ishim Anatolia_HG Magdalenian 0.001258 1.427 170086
Altai Ust_Ishim Anatolia_HG Yana 0.001374 1.972 890133
Altai Ust_Ishim Anatolia_HG Brazil_LapaDoSanto_9600BP 0.000595 0.913 800380
Altai Ust_Ishim SunghirIV Goyet 0.002215 2.526 756597
Altai Ust_Ishim SunghirIV Magdalenian 0.00148 1.656 192400
Altai Ust_Ishim SunghirIV Vestonice_all 0.001411 1.886 754276
Altai Ust_Ishim SunghirIV Yana 0.00201 2.678 1135265
Altai Ust_Ishim SunghirIV Brazil_LapaDoSanto_9600BP 0.001307 1.791 950517
Altai Ust_Ishim Goyet Brazil_LapaDoSanto_9600BP -0.000752 -0.924 717889
Altai Ust_Ishim Yana Brazil_LapaDoSanto_9600BP -0.000542 -0.935 958897

Matt said...

Denisovan, Altai, Vindija all samples that form a clade with an ancestry from Neanderthal that contributes to Eurasians in probably not equal respects, and this is proposed to relate inversely to Basal Eurasian ancestry. An opposite effect to what Chimp or African as an outgroup is supposed to achieve.

Seems like not such a useful outgroup as an alternative to Africans to detect some ancestry basal to other Eurasians?

Chimp may also have this issue though less so, since it's Basal to both DeniNeader clade and the AMH clade? Not very specific to the downstream intra-AMH splits between Eurasians and Africans. (Plus Chimp is not actually basal as I understand it, since many SNPs will be set to AMH reference when using in practice?).

See what Lazaridis says about that one. I've never seen an attempt to identify BEu ancestry by attraction to Neanderthal (or Denisovans who are a clade with them relative to AMH) compared to an ancient Eurasian reference (and I would think that would be because of this confound).

Chad said...

Africans are a not an outgroup though. Comparing stats with Mbuti Ust Ishim XY, Chimp Ust-Ishim, XY, and Chimp Mbuti show that clearly. Otherwise, you'll need to add Basal Eurasian all over to compensate. For instance Mbuti Ust Ishim Brazil LapaDoSanto Onge even says basal to Brazil. It's all a mess using African and modern Asian samples.

Matt said...

I'm sympathetic to your argument Africans and present day at that may be not a real outgroup (due to subtle geneflow or artifacts of ascertainment), but using Neanderthals and Denisovans as an alternative to detect Basal Eurasian geneflow has clear problems if the opposing hypothesis is that all Eurasians have N/N+D geneflow, and that Basal Eurasian ancestry dilutes this.

And that geneflow is settled, bulletproof science (you can't really explain any of the D(N,D;African/Eurasian,Eurasian) / D(NAltai,NVindija;African/Eurasian,Eurasian) stats without it, and there are also subtler proof). Chimpanzee may potentially have similar issues, though I'm unsure of that.

rozenblatt said...

Some off-topic: in Narasimhan's paper there was no archaeological description of Bronze Age Aigyrzhal site in Kyrgyzstan. Some description of the site can be found here: https://www.ucentralasia.org/Content/downloads/CHHU-RP3-Eng.pdf

Matt said...

@Rozen, I have literally just Ctrl+F for Aigyrzhal, it seems interesting but on their comment that: "The DNA of two buried people from kurgans #67 and #67a of Aigyrzhal-2 site were revealed in a recently-published article on the genetics of Eneolithic and Bronze Age populations on the territory of Southern and Central Asia. According to the results, these buried people were genetically linked to the people of the Botai culture in Eneolithic of Kazakhstan (Narasimhan et al., 2019). But the physical type of the buried people from Aigyrzhal-2 site was not similar to the physical type of the ancient Botai people. This is another mystery that will require further research if it is to be solved."

Their "Southern" physical type doesn't seem like a mystery judging by their PCA position and Narasimhan's data (Vahaduo custom PCA - https://i.imgur.com/AQPCL8G.png)

...

One thing that I do find interesting in Central Asia is that at Sarazm there are apparently culturally distinguishable layers where the data from "Sarazm En" samples Narasimhan had refers to a relatively earlier layer where later layers show some Afanasievo / Yamnaya related materials.

Davidski said...

@Chad

PCA means little though.

It means a lot if you know how to use and read it.

Davidski said...

@Rob

Some things are already set in stone, like the position and behavior of Pinarbasi_HG relative to many other ancients in the context of West Eurasian genetic clines.

To suggest that Pinarbasi_HG has none of the so called Basal Eurasian ancestry isn't just wrong, it's irrational.

Ryan said...

@Chad - Thanks for sharing a link to your blog. I'll add it to my reading list.

vAsiSTha said...

@davidski said "Those outgroups are obviously garbage, even though they're from a paper, because a different set of outgroups shows that they don't do the job right.

You can't get around that fact no matter what.

And there are no good models for Eneolithic_steppe, either because the right ancient populations haven't been sampled yet, or, like I just said, Eneolithic_steppe isn't really a mixed population."

Just tried your rightpops (with a couple changed, as I dont have those in my eigenstrat. you should also add Onge in your right pops & set allsnps to YES, and add satsurblia for more resolution into iran component) for caucasus_eneolithic. Caucasus_en is contemporary with steppe_en, and very proximal. The model works. Only 3 way models are accepted.
Kotias+ANF+Parkhai (parkhai=21%, p value 0.48) as well as
Kotias+ANF+Geoksyur (geoksyur=24% p value 0.68)

Result

The %s are almost same as with Wangs right pops.
Caucasus_en & steppe_en are contemporaneous and proximal.
So the above tells me that steppe_en likely fails with your right pops because of the EEHG source rather than the chg/iran source.

Rob said...

If Pinarbasi has BE then so should Villabruna

Ryan said...

@Rob - If Pinarbasi has BE then so should Villabruna

It does. I thought that was covered a year or two ago. I don't think it was Fu's paper that had that though I can't recall who did. There's both Basal Eurasian and East Eurasian in Villabruna at low levels.

Anyone able to recall which paper covered that? Was it Wang?

Davidski said...

@Rob

Villabruna might have some Basal Eurasian, but considering how it behaves in the context of ancient and modern West Eurasian genetic diversity it obviously has a lot less than Pinarbasi_HG.

Pinarbasi_HG has about as much Basal Eurasian as most early European farmers, and there's a clear difference in this context between early European farmers and European foragers, including Villabruna.

Davidski said...

@vAsiSTha

You can't chop and change outgroups to make models pass.

If a set of outgroups shows that a model has failed then you need another model not a different set of outgroups.

Duh.

Ryan said...

@All - how does the Epi-Gravettian in the area around the Black Sea (or beneath it now) sound for a source of the Villabruna cluster? A northeast to south migration in Europe that partially mirrors the latter steppe migrations?

Or am I just stating the obvious?

Rob said...

@ Davidski
Seems like you’re assuming that BE is an actual population ?

@ Ryan
No; because there was no such thing as a Villabruna migration. It’s a made-up entity

Davidski said...

@Rob

I'm not assuming anything. Even if Basal Eurasian never existed my point still stands, because it's based on the big picture of West Eurasian variation.

If you want to argue that Pinarbasi_HG is fundamentally different from the ancient samples that it broadly resembles in many different types of analyses, then you have to prove that the fundamentals are wrong.

Rob said...

Pinarbasi is fundamentally different to Anatolian Neolithic; Levant N.
It’s an upper paleolithic relict; the later incoming groups were quite different

Samuel Andrews said...

@Rob,
"Pinarbasi is fundamentally different to Anatolian Neolithic; Levant N."

What? Where did you get that from? Anatolian Neo fits as 80%+ Pinsarbi. Anatolia Neo is mostly derived from Anatolian HGs. Anatolia Neo is more similar to Anatolia HG (Pinarbasi) than Levant Neo is to Natufian.

Ryan said...

@Rob - No; because there was no such thing as a Villabruna migration. It’s a made-up entity

So the population turnover in UP Europe happened through what - magic and sunshine?

QQblog said...

Can someone point me to eigenstrat data set for Wang et al 2019 and Sikora et al 2019.

Davidski said...

@QQblog

The Wang et al. genotypes should be somewhere here.

https://edmond.mpdl.mpg.de/imeji/collections?q=#

The Sikora stuff is here.

https://sid.erda.dk/cgi-sid/ls.py?share_id=HXY5UYsqQU

QQblog said...

Thanks.

Chad said...

David,

If you argument doesn't involve any data, it is simply your opinion. That is not a sound argument. Provide evidence that contradicts this. That's the great thing about science.. it doesn't give two cents about anyone's opinion. No Basal Eurasian needed for Pinarbasi or Boncuklu. In fact. Take a gander...

Here is a tree with Mbuti added to the root.. Eurasian part holds up, but Mbuti sure have some attraction to Anatolians, Iranians, and especially Chalcolithic West Asians, as I have said, but not included.. It is African outgroups that are more unstable than Chimp.

Here is the base... Mbuti want significant admixture from Ganj_Dareh..when compared to other ancients.

https://drive.google.com/file/d/1uaPk3c5Ejwvl0yWAh_gm7ia6w-9Y1yVz/view?usp=sharing

The stats with Africans are huge when you compare modern and ancient East Asians, along with major differences in UP European and Siberian populations compared to West Asians.

With outputs: NULL on qpGraph and not including any Africans or modern Asians, the outcome of the graph is very similar to what the stats using Chimp as an outgroup are. If there is something deeper than the split of East and West Eurasians in a populations, this still picks it up. Look at Iberomaurusians, Iran, and Natufians. They had a significant need for deeper ancestry. Iran specifically asked for Iberomaurusian admixture, rather than some cryptic worse F4 (like Sunghir Ganj_Dareh ; Ust_Ishim Ganj_Dareh where it is not linked to anything in particular) where I just make the assumption that it is Iberomaurusian-related.

When you add Africans and modern East Asians to a tree from Upper Paleolithic to Neolithic, the only way to remedy this is to have significant admixture from those populations into the African population. Such as below...

https://drive.google.com/file/d/1Yzu90pcohpw8c0E-yTWntSSGHnkBOvFe/view?usp=sharing

This proves that there is some issue within the data when you combine ancient Eurasians from a large time period and these additional groups.

It is Africans driving the stats here, not Chimp. Chimp is more neutral and acts like Tianyuan here, as a real outgroup. There is nothing special about the relationship to Ust-Ishim or Tianyuan in either Anatolia_HG or SunghirIV, just as the graph without Chimp or Africans shows. They are more in-line with each other.

Chimp Mbuti.SGDP SunghirIV Anatolia_HG 0.000712 2.001 35982 35379 847590
Chimp Ust_Ishim SunghirIV Anatolia_HG 0.000044 0.062 46120 46083 845798
Mbuti.SGDP Ust_Ishim SunghirIV Anatolia_HG -0.000853 -1.281 47281 48034 882870
Tianyuan Ust_Ishim SunghirIV Anatolia_HG 0.000254 0.312 35990 35812 705443
Chimp Tianyuan SunghirIV Anatolia_HG -0.000482 -0.656 36504 36832 679816


It is safer to exclude Africans and Modern Asians when looking for true, deeper ancestry that does not fit within the Ust-Ishim, West and East Eurasian tree.

Chad said...

Another interesting little set of Dstats more in-line with my graph.. the stats regarding the relationship between Ganj Dareh, Yana, and Tianyuan. If all East Asian in Iran was via Yana, you would expect the stats with Tianyuan to be minimal compared to Yana, however the opposite is the case.. just as in the graph.

Chimp Tianyuan Natufian Ganj_Dareh_N 0.002920 4.920 23494 22284 414476
Chimp Yana Natufian Ganj_Dareh_N 0.001390 2.683 27670 26997 484580

Davidski said...

@Chad

I do have a sound argument. My argument is that whether Basal Eurasian exists or not, Pinarbasi_HG behaves in very specific and expected ways for an individual from the ancient Near East in a wide variety of basic analyses.

You've skipped past all of the basic stuff and lost yourself in a world of formal stats. Your work is highly theoretical and it lacks sanity checks, that's why you're coming up with unusual and even irrational interpretations of the data.

You need to change this ASAP.

Ric Hern said...

Which African population has the Most contribution from the Ancient Africans who split from the Lineages around 750 000 years ago which led to Modern Humans ? How much of this ancestry does Mbuti for example have ? Or was Mbuti separated from this admixture event ?

Rob said...

@ Ryan

''So the population turnover in UP Europe happened through what - magic and sunshine?''

of course not, but it actually entails 3 or 4 separate but interlinked events. What has been dubed 'the Villabruna process' is called by the rest of academia 'the Azilianization of Europe'; it wasnt a migration from Near East, or Black Sea

vAsiSTha said...

@davidski said "@vAsiSTha

You can't chop and change outgroups to make models pass.

If a set of outgroups shows that a model has failed then you need another model not a different set of outgroups.

Duh."

I used your outgroups with my modifications(becuse i dont have all your rightpops) to test both steppe_en and caucasus_en. 1st failed, 2nd worked. caucasus_en is modeled successfully with the same left pops even using Wang's right pops.

Now do this and show us the results - Use the rightpops that you used with steppe_en failed model for caucasus_en, Kotias, Anatolia_N, Parkhai/Geoksyur left pops.

I will list your own rightpops for you
Mbuti,MAR_Iberomaurusian,IRN_Ganj_Dareh_N,Levant_PPNB,Anatolia_Barcin_N,Iberia_Southeast_MLN,RUS_MA1,RUS_Ust_Ishim,RUS_Kostenki14,RUS_Karelia_HG,SRB_Iron_Gates_HG,RUS_Kolyma_Meso,BRA_LapaDoSanto_9600BP,Iberia_Northwest_Meso

Anatolia_Barcin_N will need to be replaced because it is in left pops.

Im 99.9% sure model will work. And then you could tell us why it works for caucasus_en but not for steppe_en. cant let you wiggle out of this.

Chad said...

Trust me, bro... I have a better feeling about this than the other stuff I picked out.. It was an artifact with African populations vs ancient Eurasians that was causing the issue. This will hold up, as well as there being actual Ust_Ishim ancestry in Goyet, Magdalenians, and Yana. This was transferred to later Meso hunters, which is why you see all of them and Azilians closer to Ust Ishim than older UP Euros or Epipaleolithic Anatolia.

AWood said...

So what's the difference betweeen the "southern" type and the "uraloid" type that I see mentioned in these Russian steppe papers all the time, where there are 2 or more distinct "types". Does the southern type refer to the "gracile dolichocephalic mediterranean" that is often referenced when discussing the early European farmers, or something else? If so, what does that make the so-called "uraloid"? A more robust type of some sort?

Kristian Kristiansen said...

Thanks for this interseting blog. Concernig Maykop and Yamnaya origins let me kristian kristiansen explain tjat I do not infer a fenetic origin from Maykop toYamnay, I propose a culturlaæ and perhpas linguistic influence from the highly developed Maykop to the much less deceloped early Yamnaya
Kristian kristiansen

Davidski said...

@Kristian Kristiansen

Yes, I understand that this is a continuation of your earlier work based purely on archeological data.

However, my point was that we now have the relevant ancient DNA data from Maykop sites, and it contradicts the inferences from archeological data that there may have been rich cultural and linguistic ties between Maykop and Yamnaya.

For me it suggests the following things:

- the Maykop and Yamnaya groups were genetically highly distinct and they didn't mix, so it's unlikely that their languages were related or that the Yamnaya people eventually adopted the language of the Maykop people

- the Steppe Maykop population seems to have totally disappeared before, during or just after the Yamnaya people moved into the steppes north of the Caucasus, so it's possible that these groups were in a hostile relationship with each other, and makes it likely that the Steppe Maykop language also totally disappeared from the steppe.


John Rudmin said...

My contribution is total childish amateurism, but just guessing that Greek IE descends from Badin culture. Perhaps first a Luwian-related wave from the more easterly Ezero branch of Badin, and then perhaps the proto-eu-Hellens filter in through Dinaric northwest, perhaps more related to Vucedol? Just a guess.

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