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Monday, December 21, 2015

Bronze Age steppe warrior affinity test


Reich Lab et al. are now targeting more than 1.2 million sites in the ancient samples that they genotype, including over one million from the Illumina genotype array. This is great because it means that I can now run analyses with these ancients on the present-day populations in my Illumina array-based dataset using as many as 500K SNPs, which makes things more accurate and interesting.

Below are a few sets of D-statistics of the form D(Outgroup,X)(Population1,Population2), featuring several ancient populations from the recent Allentoft et al., Haak et al. and Mathieson et al. papers. I'm basically testing how much closer X is to either Population1 or Population2.

The results look very solid considering the spatio-temporal and archaeological origins of the samples. However, the outcomes for the smaller Northern European nations perhaps look slightly inflated. This is probably due to their peculiar demographic histories and resulting relative genetic homogeneity. At this stage, I don't know how to test this and limit its effects, if indeed it is a problem.

Afanasievo
Poltavka 0.4678
Yamnaya_Kalmykia 0.4667
Yamnaya_Samara 0.4659
Srubnaya 0.4583
Corded_Ware_Germany 0.4554

Full output here

Andronovo
Sintashta 0.4584
Poltavka 0.4571
Srubnaya 0.4566
Yamnaya_Samara 0.4556
Afanasievo 0.455

Full output here

Khvalynsk
Poltavka 0.4617
Yamnaya_Samara 0.4594
Afanasievo 0.4556
Yamnaya_Kalmykia 0.454
Srubnaya 0.4522

Full output here

Poltavka
Yamnaya_Samara 0.4658
Afanasievo 0.4616
Yamnaya_Kalmykia 0.4602
Corded_Ware_Germany 0.4555
Srubnaya 0.4551

Full output here

Poltavka_outlier
Srubnaya 0.4572
Poltavka 0.4568
Sintashta 0.4534
Yamnaya_Samara 0.4518
Corded_Ware_Germany 0.4514

Full output here

Potapovka
Poltavka 0.4555
Srubnaya 0.454
Andronovo 0.4537
Yamnaya_Samara 0.4536
Corded_Ware_Germany 0.4523

Full output here

Sintashta
Andronovo 0.4567
Srubnaya 0.4553
Poltavka 0.4526
Yamnaya_Kalmykia 0.4507
Unetice_EBA 0.4506

Full output here

Srubnaya
Poltavka 0.4571
Yamnaya_Samara 0.4565
Afanasievo 0.454
Corded_Ware_Germany 0.4538
Unetice_EBA 0.4528

Full output here

Yamnaya_Kalmykia
Afanasievo 0.4644
Poltavka 0.464
Yamnaya_Samara 0.463
Srubnaya 0.4523
Andronovo 0.4513

Full output here

Yamnaya_Samara
Poltavka 0.4669
Yamnaya_Kalmykia 0.4615
Afanasievo 0.4612
Srubnaya 0.4554
Corded_Ware_Germany 0.4542

Full output here

See also...

qpAdm tour of the Eneolithic/Bronze Age steppe

At least three genetically distinct Indo-European migrations into South Asia

15 comments:

Shaikorth said...

"At the same time, however, the outcomes for the smaller Northern European nations look slightly inflated. This is probably due to their peculiar demographic histories and resulting relative genetic homogeneity. At this stage, I don't know how to test this and limit its effects, if indeed it is a problem."

The inflation of Kalash D-stats towards Brahui in a similar test was detectable by comparing their IBS sharing with Brahui (not elevated) to their D-stat result, you might want to try testing IBS sharing with ancients using these same SNP's.

Regarding the effect of homogenousness in particular, I guess the way to test that would be to check the internal IBS-sharing of every modern sample, or maybe just modern North, East and Central European sample in this case. Then check the sample's two individuals with highest and lowest IBS sharing with ancients, heterogenous populations should show a wider gap between these two but the "highest" sharer might be above those in homozygous pops.

Krefter said...

@Davidski,

Do all LNBA North Europeans, including Nordic LNBA and the Urnfield guy, have more Steppe than modern North Europeans? Are most Bell beaker more Steppe than Unetice? Is Unetice more Steppe than Nordic LNBA? Is Nordic LN more Steppe than Nordic BA and IA? Are the Bell Beaker the least homogeneous LNBA European group?

Davidski said...

The Nordic LNBA samples aren't very homogeneous. Some show a lot more steppe ancestry than modern Scandinavians, and others much less. But overall, Nordic LNBA shows a little more steppe ancestry than modern Scandinavians. You can see that here, because it's a little higher than Norwegians and Swedes.

https://drive.google.com/file/d/0B9o3EYTdM8lQWDR0WThZM1FEaVU/view?usp=sharing

https://drive.google.com/file/d/0B9o3EYTdM8lQWk03cGVxa2s4TjA/view?usp=sharing

https://drive.google.com/file/d/0B9o3EYTdM8lQcURUQzc0M01uMTg/view?usp=sharing

The Urnfield individual also has a little more steppe ancestry than modern North Euros. He's actually very similar to Sintashta, which is interesting, considering he's also R1a.

Krefter said...

It's surprising 1800 years after arrival some were still overwhelmingly Steppe. Do you think it is only WHG and EEf which is pulling modern Northern Europeans further away from the Steppe, or also excess CHG? Does 50-70% replacement levels in Scandinavia and British Isles by Eastern/Steppe(admixed with MN) populations sound realistic?

Coldmountains said...

Something is very odd here. How have some Ukrainians, Kargopol Russians and Erzya less affinity to Sintashta than French Basques? Many results for East Europeans look very odd.Homogeneity of some West Europeans and non homogeneity of many East Europeans makes this lists inaccurate.

Davidski said...

Admixture from highly divergent sources like East Asia dampens affinity to the steppe populations.

Kargopol Russians and Erzya have around 6% Siberian admixture, while Sintashta has 0%. At the same time, Sintashta shares a lot of ancestry with Basques via EEF, CHG and even EHG.

So the results are accurate.

Coldmountains said...

@Davidski

Ok that makes sense for siberian-admixed people but why are Ukrainians also so low in this list. Lower than Slovakians, all West Europeans and even Slovenians? Russians and Belarusians are also lower in the list than I would except.

Coldmountains said...

@Davidski

Erzya and Moksha were also quite low in the list for Volga Scythians and NW Europeans highest but these Scythians had unlike Sintashta indeed some Siberian admixture.

Davidski said...

Most Ukrainians have more Southern European admixture than more northerly Balto-Slavs. This probably affects their results here.

And I don't think Belarusians, Russians and Ukrainians from Belgorod are lower on these lists than I'd expect them to be. They're actually pretty high up on some of the lists.

In reality the differences are pretty small here between all Northern Europeans from Ireland to Russia, so the fact that one country is above another doesn't say much.

Not sure why the Scythian affinity doesn't peak in the Volga area? But IBS and formal stats show pretty much the same thing, so it has to be around the mark.

Coldmountains said...

Yes that is obvious from admixture and the more southern location of Ukraine. I was not questioning that but rather how Poltava Ukrainians have less or the same Sintashta affinity like French Basques. Here Ukrainians look often more southern than Slovakians and even Slovenians what is rather surprising for me. Ukrainians should have similar amounts of Steppe admixture like Irish, Scots and some Norwegians and Belarusians and Russians should have a bit more steppe admixture than Norwegians based on their higher EHG.


It is strange that Scythian affinity is according to this not peaking in the Volga region today, where scythian Z2123 is still found unlike in the rest of Europe and where Scythians had a very very long presence. I still have my doubts about Scythian affinty being higher in NW Europe than in the Volga region. Scythians left hardly any descendants in Europe outside of the Volga region and were very Siberian admixed compared to most modern Europeans. So their admixture proportions should be similar to Erzya/Moksha/Kargopol Russians .

Davidski said...

It's an interesting question why the affinity even to Scythians is dampened in far Eastern Europe.

It might have something to do with CHG ratios, which are relatively high in NW Europe and parts of East Central Europe.

Coldmountains said...

CHG is higher in The Balkan, Ukraine and not low in The Volga Region. Actually admixture (CHG K8 on anthrogenica) showed that it is not higher in NW Europe and quite high among Volga people. The ratio of EEF/CHG is much higher in West Europe than in East Europe. Tatars with confirmed direct scythian ancestry (They carry R1a-Z2123 like Scythians and absent in the rest of Europe) have lower or the same affinity to Volga Scythians than Albanian and Spaniards here. That is really against any common sense especially because these Scythians had a lot Siberian admixture absent among almost all other Europeans . Admixture clearly showed that these Scythians were basically like modern Tatars but with a higher CHG and EHG affinity and that makes quite much sense.

Tesmos said...

Which Dutch samples are included? A mixture of North and Southern Dutch?

Davidski said...

Coldmountains,

There might be other components in the Volga region brought in by Turks recently that are causing the problems. I'll check this out when more Scythian samples come in.

Tesmos,

They're something like 3/4 north Dutch and 1/4 south Dutch.

Coldmountains said...

@Davidski

Anyways thanks very much for your analysis. It is a mystery and something almost in all of Far East Europe is dampening the affinity. Volga Finns who should have similar admixture proportions,who lack significant altaic admixture and who have a lot of EHG for modern european standards, are also much lower in the list than i expected. So either something is inaccurate or something which effected all of East Europe lowered the affinity but i dont think it were Altaics because Volga Finns dont seem to have that much altaic admixture like Russians who also basically lack it. Admixture, which is probably not always reliable, rather showed that the closest population to modern Scythians were Volga Finns, Tatars and Far East Europeans (lithuanian-like with siberian admixture) but yes you are right without more genomes we can not solve this mystery.