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Tuesday, June 2, 2020

Perhaps a hint of things to come


It's still a mystery how the Hittites and other Anatolian speakers ended up in the Near East. However, the leading theory is that their ancestors migrated from the steppes of Eastern Europe to western Anatolia via the Balkans sometime during the Copper Age.

Consider the qpAdm mixture models below, made possible thanks to some of the ancient samples published recently along with Skourtanioti et al. 2020. The key ancients are described in a text file available here.

TUR_Barcin_C
AZE_Caucasus_lowlands_LN 0.471±0.094
RUS_Vonyuchka_En 0.148±0.040
TUR_Barcin_N 0.381±0.069
chisq 12.874
tail prob 0.116261
Full output

TUR_Barcin_C
RUS_Vonyuchka_En 0.107±0.029
TUR_Buyukkaya_EC 0.893±0.029
chisq 12.107
tail prob 0.207331
Full output

I'd say it's quite clear now that TUR_Barcin_C harbors minor ancestry from the Pontic-Caspian (PC) steppe. The reason this isn't widely accepted yet is because demonstrating it convincingly hasn't been possible without a proximate Anatolian ancestry source for TUR_Barcin_C, precisely like TUR_Buyukkaya_EC.

Admittedly, though, the statistical fits in my models aren't all that great. I suspect the problem lies with RUS_Vonyuchka_En, which is likely to be a rather poor stand in for the people who brought steppe ancestry, and possibly early Anatolian speech, to western Anatolia.

So let's see what happens when I try a more proximate reference for the steppe ancestry in TUR_Barcin_C. How about Yamnaya_BGR, an individual of mixed Balkan and steppe origin from what is now Bulgaria?

TUR_Barcin_C
AZE_Caucasus_lowlands_LN 0.518±0.075
TUR_Barcin_N 0.203±0.056
Yamnaya_BGR 0.279±0.067
chisq 10.602
tail prob 0.225269
Full output

TUR_Barcin_C
TUR_Buyukkaya_EC 0.749±0.058
Yamnaya_BGR 0.251±0.058
chisq 9.687
tail prob 0.376414
Full output

That's a little better. Unfortunately, the problem now is that the models are anachronistic, because TUR_Barcin_C is about a thousand years older than Yamnaya_BGR. Clearly, we need more Copper Age samples from the western edge of the PC steppe, the eastern Balkans, and especially northwestern Anatolia.

The Principal Component Analysis (PCA) below effectively illustrates why my qpAdm models work. It was produced with Global25 data using the Vahaduo PCA tools freely available here. Note that TUR_Barcin_C is shifted away from the essentially perfect cline formed by AZE_Caucasus_lowlands_LN, TUR_Barcin_N and TUR_Buyukkaya_EC towards samples from ancient Eastern Europe, including Yamnaya_BGR.


See also...

Steppe invaders in the Bronze Age Balkans

230 comments:

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Jatt_Scythian said...

I also read somewhere the SNPs do indicate Tianyuan is ancestral to Yana who is ancestral to Malta.

Anonymous said...

@Jatt_Scythian

The branches have nothing to do with this, at that time (>30000BP) there were no East Asian and West Asian branches yet, they will be formed later as a result of population isolation. The Tianyuan is a more East Asian specimen because its mitohaplogroup is East Asian B. They are separated by mitohaplogroups, not by Y-haplogroups. These populations are much closer to each other than East Asians and West Asians. K2b is not East Eurasian, because C1a is not West Eurasian. The fact of East Eurasianity in Tianyuan is its East Asian mitohaplogroup, not the Y-haplogroup.So, ANI EXCAVATOR is completely unconvincing.

Tianyuan has a recent northern Denisovan admixture from the Altai, not southern.

Jatt_Scythian said...

If he has Northern Denisovian ancestry and not southern that would only preclude him from being SE Asian like though no? He could still be NE Asian like?

Where did the eastern admixture in Yana come from though if not the ydna since both samples + Malta were all mtdna U? Sure its possible the broader Yana and Malta populations had Eastern mtdnas too and we just didn't find them but there's nothing that would back that up at the current time.

I'm confused either way. On one hand I see arguments for a SE Asian origin but Tianyuan being at the top of the tree and having the ancestry that separate NE Asians from SE Asians would argue against that.

Jatt_Scythian said...

Isn't the split of East - West close to ~48k ybp? Since K2b is only slightly older than Tianyuan its guess its possible K2b was originally crown eurasian before ending up on the east asian side but You're saying there were crown eurasians running around till 30K ybp?

Ric Hern said...

@ Archi

I think that Hindu-Kush to Altai makes sense. North Central Asia and Southern Siberia is where things happened especially for K2b. Earlier K maybe were spread from Northwestern Iran to Afghanistan...

ANI EXCAVATOR said...

@ Archi

The paper you are pulling quotes from has only East Asians from 9 thousand years or younger. It tells us nothing about the origins of East Asians.

At the time humans reach East Asia and Oceania, three groups of Denisovans existed: D2 in Southeast Asia, D0 in the Altai and D1 in Oceania. East Asians and Tianyuan have D0 from the Altai Denisovans, but Papuans and Australians do not have this ancestry. East Asians and ASI do have the D2 ancestry that Papuans have, but less than their D0 ancestry. Only Papuans and Australians have D1. Its not clear from this paper whether Tianyuan or Salkhit have traces of D2 like modern East Asians have, only that most of their Denisovan is not from D2, like East Asians today.

East Asians, Papuans and Australians, and ASI separated a very short time before Tianyuan. Because East Asians don't have D1 and Papuans don't have D0, and maybe Tianyuan and Salkhit don't have D2, but the ancestors of East Asians, Papuans, Salkhit and Tianyuan were basically the same people when they first reached East Asia and Oceania, the admixing probably happened with local groups of Denisovans after each group of humans settled there and can't be used to trace the route each group took.

Jatt_Scythian said...

@Ric Hern

What is that based on? The only K2b we have is from NE Asia.

Its possible IJK or K1 did originate in that area but those might be from east asia too according to some people but I'm not too sure.



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On a related note what languages and ydnas were predominant in the Northern person of European Russia before Uralic showed up to the scene?

Jatt_Scythian said...

Ric Hern

There isn't much K2 in those regions.

ANI Exacavator
So South Asians have D0 and D2 ancestry? Do you know much?

ANI EXCAVATOR said...

@ Jatt

"On one hand I see arguments for a SE Asian origin but Tianyuan being at the top of the tree and having the ancestry that separate NE Asians from SE Asians would argue against that."

Not really a Southeast Asian origin, just a route to Siberia that went through people related to later East Asians and Oceanians.

The important thing is that East Asians, Papuans and Australians, and ASI were basically the same group of people just before Tianyuan existed, who colonized East Asia and Oceania. The fact that one group of people crossed into East Asia, then split with one group going to Oceania, one going North to Northeast Asia and another staying as hunter-gatherers in Southeast Asia and India shows that the likely route is southern, not northern.

The fact that Ust-Ishim and other ancient Siberians are not related to East Asians and do not have Denisovan ancestry, except when admixed with East Asians, also shows that East Asians did not take a route from the Hindu Kush to the Altai through Central Asia or Siberia, but went south of the Himalayas.

@ Archi

"The branches have nothing to do with this, at that time (>30000BP) there were no East Asian and West Asian branches yet, they will be formed later as a result of population isolation."

Not true. Populations ancestral to East and West Eurasians had already split when Tianyuan lived, and probably even earlier around 50 thousand years ago.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3568306/:
" The nuclear DNA sequences determined from this early modern human reveal that the Tianyuan individual derived from a population that was ancestral to many present-day Asians and Native Americans but postdated the divergence of Asians from Europeans."

"The Tianyuan is a more East Asian specimen because its mitohaplogroup is East Asian B. They are separated by mitohaplogroups, not by Y-haplogroups. These populations are much closer to each other than East Asians and West Asians. K2b is not East Eurasian, because C1a is not West Eurasian. "

Whether or not an ancient sample is part of any group is determined by its autosomal DNA, not by its haplogroups. Like you said, the fact that some West Eurasian people had C1a does not turn them into East Asians.

Anonymous said...

@Ric Hern "Earlier K maybe were spread from Northwestern Iran to Afghanistan..."

Rather, Northern India, because its other branches (M,S,K3) all went south to Southeast Asia.

Anonymous said...

@ANI EXCAVATOR

"Not true. Populations ancestral to East and West Eurasians had already split when Tianyuan lived, and probably even earlier around 50 thousand years ago."

No it's true, Goyet confirms it. So you are wrong just in fact.

"Whether or not an ancient sample is part of any group is determined by its autosomal DNA, not by its haplogroups."

hat's exactly what I'm talking about, you based on autosomes attributed k2b East Asian origin, and this is just the spread of this haplogroup further to the East. While the true carriers of Eastasiaticism here were precisely female lines, that is, you confuse cause and effect.

You divide too primitively - East Asians and West Asians and nothing more. There was no such thing, anthropologists have long decided that everything was much more complex and gradual.

Jatt_Scythian said...

@ANI EXACAVATOR

WHat would have been the yndas of those South Asian Hunter gatherers (ASI)? C1b (old C5) and H?

@Archi
If that were true wouldn't it still make them East Eurasian? I doubt India had West Eurasian (or even crown Eurasian) influence back then?

Jatt_Scythian said...

On a somewhat related note what was in the Altai, South Siberia and Tarim Basin when IE speakers expanded there?

Jatt_Scythian said...

I'm still confused. So no SE Asian origin but the diversity of K2 is there. If K went south and east of the Himalayas and then north to NE Asia (where K diversified into K2 and ultimately gave rise to Tianyuan) was found shouldn't he have some sort of Southern Denisovian ancestry? Are we suggesting all branhces of K2 originated in a Tianyuan like population but today are only found among Anadaman islanders and other island SE Asians?

Ric Hern said...

@ Archi

So do you propose LT also spread from Northern India ? LT is why I said between Northwestern Iran and Afganistan...

Anonymous said...

@Ric Hern

All K, F branches are from Northern India. L and T are in eastern India.

https://upload.wikimedia.org/wikipedia/commons/0/09/Haplogroup_LT_%28L298-P326%29.png

https://upload.wikimedia.org/wikipedia/commons/5/5b/Y-Haplogroup_Paleolithic_Migrations.png

Jatt_Scythian said...

The majority of K2 is in SE Asia. The only modern F is in SE Asia but I don't think it originated there so I agree with you.

How can your prove something with modern frequencies and a map?

I'd be very surprised is L and T aren't from Iran. L is likely a good candidate for the Iran_N component imo.

Jatt_Scythian said...

Also was NW Russia mostly EHG before Uralics? What about South Siberia and the Tarim before IEs? WSHG and Iran_N/ENA respecitvley?

Rob said...

It doesn’t matter which route around the Altai the predecessors of TY took. to claim that his population is somehow west Eurasian is is trying to square a circle
In a qpGraph set up; TY branches with ancient samples from Vanuatu, So it doesn’t matter if Andamanese “can walk naked in the cold” lol

Archi wrote a lot of disinformation about UP Europe - people should refer to figure 2 here
https://www.biorxiv.org/content/10.1101/2020.06.03.131995v1.full.pdf

Anonymous said...

Rob writes the same nonsense as always without understanding the subject. There's no qpGraph with Vanuatu there, and qpGraphs don't prove anything at all, they're purely subjective. Especially if they are simplified. All the more so when they exclude Ust-Ishim and Oase1 and Oase2 as contradictory to their paradigm. But it's a fact, see dates:

F formed 65900 ybp, TMRCA 48800 ybp
GHIJK formed 48800 ybp, TMRCA 48500 ybp
H formed 48500 ybp, TMRCA 48500 ybp
IJK formed 48500 ybp, TMRCA 47200 ybp
IJ formed 47200 ybp, TMRCA 42900 ybp
K formed 47200 ybp, TMRCA 45400 ybp
LT formed 45400 ybp, TMRCA 42600 ybp
K2 formed 45400 ybp, TMRCA 45400 ybp
K2b formed 45400 ybp, TMRCA 44300 ybp
Palaeolithic China Tianyuan Cave, Zhoukoudian cave system, Beijing [Tianyuan 1] 38170-36880 calBCE (34430±510 BP, BA-03222) M K2b B
K2b1 formed 44300 ybp, TMRCA 44300 ybp
P formed 44300 ybp, TMRCA 41500 ybp
P1 formed 41500 ybp, TMRCA 30700 ybp
Palaeolithic Russia Yana river, north Siberia [Yana1] 32047-31321 cal BP (27940 ± 115 BP) M P1
Palaeolithic Russia Yana river, north Siberia [Yana2] 32047-31321 cal BP (27940 ± 115 BP) M P1

Rob said...

How compelling..

Jatt_Scythian said...

Does anybody have the contact info for the uses Ebizur and Shaikoroth? They always provided informative unbiased analysis so I'd be curious on their opinion on this issue.

ANI EXCAVATOR said...

There is nothing subjective about qpGraph. It uses a matrix of all possible f2, f3 and f4 statistics between all populations in the graph for the fit, so information from any f or D statistic you can think of has already been accounted for in the graph.

The problem is, not every single graph shape would have been tried for big graphs with many populations, there are too many graph shapes to try. But most of the graph shapes we are talking about are small, possibilities are explored quickly.

If we do not accept qpGraph, we can look at Treemix. You do not have to specify a tree shape for that, the best shape is automatically generated.

When Treemix and qpGraphs come to the same conclusion, it is strongly supported. Treemixes and qpGraphs from various papers have all supported the next two points:

The reason why Goyet shares drift with East Asians is because it has ancestry from Tianyuan type people, just like Yana did.

Around 40 to 35 thousand years ago, 3 groups existed: Oase and Ust Ishim type people, who did not leave any descendants, which other than qpGraph and treemix is also shown by how they are equally related to everyone. Kostenki and Sunghir type people, who are ancestors of West Eurasians, and are clearly shifted to them. And Tianyuan type people, who are ancestors of East Asians, ASI and Oceanians, and also show a closeness to them.

So Kostenki and Sunghir, and Tianyuan, don't behave like Oase and Ust Ishim at all, and instead of just a gradual pattern we clearly see three groups that behave very differently in different kinds of genetic analysis.

Anonymous said...

ANI EXCAVATOR said...
"There is nothing subjective about qpGraph."

Nothing like that, just the form of the graph is subjective, what kind of results you set and get. If you have not set the right form, you will not get the right results. That's the thing, qpGraph can not prove anything, can not refute anything.

About the fact that at that time the concept of Western Eurasians and Eastern Eurasians is wrong, in the first they are not displayed in the modern population of these concepts, the second form a close relationship between themselves, in the third have many intermediate states. These populations are closely related to each other as Europeans. In anthropology they are called the Northern Anthropological Formation, which existed before the real division into Western Eurasians and Eastern Eurasians.

Jatt_Scythian said...

If it ends up K2b (and therefore P and R) are East Eurasian as it is looking then wtf is all the chest beating about R1b on sites like Anthrogenica and Eupedia about? Those people probably look down on haplogroups like G, H, J, L and T which are actually likely to be associated with West Eurasians.

Jatt_Scythian said...

Also how much ENA is there in WHG and ANE? I'm guessing the former has ENA because of y C in some samples?

Jatt_Scythian said...

What do you guys think of the idea that ANE was originally y C1a and that y K2/P/R represent ENA introgression and wiped out the C1a guys?

RobertN said...

@ANI EXCAVATOR

"The reason why Goyet shares drift with East Asians is because it has ancestry from Tianyuan type people, just like Yana did."

Pardon me for my obtuseness. I'm a layman. Do you mean here that this shared drift is due to admixture from Tianyuan people, or is it due to the common ancestry both shared prior to splitting off from one another.

Thanks.

Jatt_Scythian said...

Can someone educated in y dans confirm if these studies are accurate?

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4755386/

22% R,11% H,4% J,2% L,1% G - Seems very weird for a Tibetan population.

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https://www.nature.com/articles/s41598-020-59061-9

Ladakh only has R1a, L, Q, J1, R1b and I2a1?

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https://www.sciencedirect.com/science/article/pii/S0002929707625075

Also do difference in ydna between Batli speakers and Indo-Aryan speakers in Pakistan?

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What does this suggest about the peopling of this region?

Jatt_Scythian said...

Yea no way everybody got it wrong on Tianyuan being East Asian. K2b is East Asian unless it also pops up in a West Eurasian population at the same time which I doubt will ever happen.

In terms of South Asia who would have thought tribals with y H are actually the ones who might have a West Eurasian ydna (in terms of deep ancestry) and R1a is the lineage that ultimatley has an ENA ancestor? Genetics is crazy.

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