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Saturday, June 23, 2018

Guest post: we owe many of our genetic traits to ancient steppe pastoralists, but...


This is a guest post courtesy of Samuel Andrews, a regular commentator for several years at this blog. I did edit parts of the original text submitted to me, but these were just cosmetic changes. If you spot any issues with this article, feel free to complain to Samuel in the comments below.

Massive migrations of pastoralists from the Pontic-Caspian steppe in the 3rd millennium BC abruptly ended generations of genetic stability in Europe. These large-scale population movements spread Yamnaya and Yamnaya-related ancestry throughout most of the continent, and indeed also much of Eurasia. Moreover, they also carried a specific type of European farmer ancestry, which was picked up by the migrating herders just west of the steppe.

By the end of the 3rd millennium BC, people across long distances within Europe shared very recent ancestry from the Pontic-Caspian steppe and surrounds. As a result, far away locations in Europe were more connected than they were ever before.

Ancient genome-wide data suggest that these migrations also spread unique genetic traits, such as lactase persistence and fair hair (blonde & red), that were once mostly restricted to a fairly limited region within Europe. However, some of these traits were originally derived from the farmers, or rather agropastoralists, who lived just west of the steppe, such as the Globular Amphora and Funnel Beaker peoples, rather than the steppe herders, and indeed this appears to be the case for both lactase persistence and fair hair.

In the 3rd millennium BC, both of these traits went from relative obscurity to widespread prominence across and beyond Europe. The Bell Beaker people, who dominated the western half of Europe during the Early Bronze Age (EBA), and the Sintashta people, who, soon after, lived just east of Europe's present-day border in the Trans-Ural steppe of what is now Russia, demonstrate this well.

The pre-Sintashta and pre-Beaker populations of present-day Russia and Britain, respectively, showed low frequencies of alleles associated with fair hair. Thus, the Beaker and Sintashta peoples took high frequencies of these alleles, which they both probably inherited from Eastern European farmers, to the opposite ends of Europe, and then, via the expansions of Sintashta-related Andronovo populations, also deep into Asia.

rs4988235 > lactase persistence
rs16891982 > light skin & blonde hair
rs12913832 > blue eyes & blonde hair
rs1805008 > red hair


When the Andronovo groups mixed with the indigenous inhabitants of Asia, the frequencies of most of these European-specific alleles among them were reduced, until they almost disappeared in the new populations that formed as a result of this mixture process. Nevertheless, they continued to exist wherever there was significant Andronovo ancestry, including in the Iron Age peoples of the Swat Valley in what is now Pakistan:

Swat Valley, Udegram_IA, S8195.E1.L1; allele T at rs1805008 (aka R160W), the most popular red hair variant among present-day Europeans.

Swat Valley; 17% derived allele frequency at rs16891982; 11% at rs12913832; twice as much as what Neolithic, Chalcolithic, and Bronze Age South Central Asians could boast.

Swat Valley, Barikot_IA, I6547; allele A at rs4988235 (aka I3910-T), the main lactase persistence mutation in both present-day Europe and South Asia.

Hence, I3910-T is a direct link between the populations of the Iron Age Swat Valley and ancient Europe. Indeed, Ukraine_Eneolithic I6561, from a burial associated with the Sredny Stog II archaeological culture in the North Pontic steppe, present-day Ukraine, is the oldest, UDG-treated sample in the ancient DNA record to date to show I3910-T. And he's also the oldest individual to belong to Y-chromosome haplogroup R1a-M417, which is today one of the most common Y-chromosome haplogroups in both Eastern Europe and South Asia, especially among the speakers of Indo-European languages.

After its expansion from Eastern Europe, I3910-T was heavily selected for both across most of Europe and in large parts of South Asia. Today, its frequencies vary significantly by region and ethnic group in India. By and large, much like R1a-M417, it’s more common in Indo-European-speaking North Indians than Dravidian-speaking South Indians. But it clearly peaks in Indian pastoralist populations that consume a lot of dairy products. They carry I3910-T at frequencies equal to those seen in many European groups.

The red hair variant R160W, seen in Swat Valley sample S8195.E1.L1, is another direct link between ancient South Asia and Europe. Just like I3910-T, R160W has been shown to have been present in Europe at least 2,000 years before the Andronovo Culture. Balkans_ChL I2423, a sample from what is now Bulgaria, carries R160W. This individual dates to 4400 BC, so he's of a similar age to Ukraine_Eneolithic I6561, the above mentioned early I3910-T carrier from the North Pontic steppe.

Other than that, as things stand, R160W is absent from pre-Kurgan Europe. In the aftermath of the Steppe migrations, around 2400-1800 BC, R160W pops up in many places in Europe just like I3910-T does. Four Andronovo/Sintashta samples out of about 100 carry R160W. Thus, a few, perhaps 1%, of the Andronovo and Sintashta people almost certainly had red hair.

Though very rare, R160W and other red hair variants do exist in South and Central Asia today. Several South Asians from the 1000 Genomes dataset carry R160W (see here). A Pathan or Pashtun from the HGDP dataset is predicted to have red hair by HIrisPlex-S. There is little doubt that this is associated with their Andronovo ancestry.

Main data sources...

Lazaridis et al. 2016

Lipson et al. 2017

Mathieson et al. 2018

Narasimhan et al. 2018

Olalde et al. 2018

See also...

Yamnaya isn't from Iran just like R1a isn't from India

56 comments:

Santosh said...

@Samuel Andrews - So these features where not carried South of the caucuses and anotolia during that time period?

Ric Hern said...

@ Samuel Andrews

How does the Steppe Mesolithic samples compare to the Steppe Eneolithic samples in these respects ?

Ric Hern said...

@ Samuel Andrews

Would it be accurate to say that these mutations were mostly transfered via the females ?

Samuel Andrews said...

There's not a lot of samples from steppe eneolithic or Mesolithic. So far shg and ehg are mostly derived for slc45a2 unlike yamnaya.

It was probably mostly female mediated. Even Latvians might have mostly farmer mtdna (it matches globular best). But we don't know the details. Patrilineal clan complicate it. Plus, there's i1 which may be a farmer/hg lineage.

In western Europe though r1b beaker folk introduced these traits. In that case it wouldnt be female mediated.

Folker said...

On Anthrogenica, Angle has successfully with a taî of 0,999618 as a 4-mix:
EHG
CHG
Trypillia
Ukraine Neolithic

It is very coherent with archeology.

So it could be best to search the variants in CT instead of GAC.

jv said...

Yes! R1a-M417 L664 redheaded Great Grandfather with origins from Scotland to Colonial New England.

Eric Wilds said...

So what is the geographic demarcation that divides WHG from EHG?

Matt said...

@Folker, the proportions are a little odd though CHG 30%, Trypillia 7%, Ukraine_N 9%, EHG 54%.

Slotting them into a simple Fst+PCoA model of ancient Eurasians: https://imgur.com/a/FFbeT4z

Seems too displaced towards European HG in the simple pan-Near East vs pan-European HG dimension, where Yamnaya is about half as Near Eastern as CHG.

You could slot into the Global25 and I think you'd see the same thing. Wang's Fig 4 gives Yamnaya Samara as no more than 51% EHG+WHG, not 63%.

Davidski said...

@Folker

Yamnaya might indeed have admixture from Trypillians, but I'm pretty sure that Beakers and Sintashta have admixture from Globular Amphora.

Apart from that I think there might be something lacking in Angle's qpAdm outgroups, hence those sensationally good fits.

@Eric Wilds

There was no clear demarcation line between WHG and EHG. They're part of a cline of European forager populations that gradually goes from WHG to EHG.

Ryan said...

I guess you should fear my all-conquering red Beaker-beard.

bellbeakerblogger said...

Looks good Sam

Chad Rohlfsen said...

Folker,

That mix doesn't really work on qpAdm. Ukraine_N was long gone anyway.

left pops:
Steppe_EMBA
EHG
CHG
Ukraine_N
Trypillia

right pops:
Mbuti_DG
Ust_Ishim
Kostenki14
ElMiron
GoyetQ116-1
Villabruna
West_Siberia_N
MA1
Levant_N
Ganj_Dareh_N
Kennewick
Ami
Anatolia_N
Balkans_N

numsnps used: 145671

best coefficients: 0.472 0.426 0.028 0.074
std. errors: 0.046 0.028 0.056 0.032

fixed pat wt dof chisq tail prob
0000 0 10 5.134 0.882054 0.472 0.426 0.028 0.074
0001 1 11 10.456 0.489922 0.416 0.476 0.108 -0.000
0010 1 11 5.585 0.899554 0.494 0.423 -0.000 0.083

Using just Trypillia

left pops:
Steppe_EMBA
EHG
CHG
Trypillia

best coefficients: 0.493 0.422 0.084
std. errors: 0.018 0.028 0.025

fixed pat wt dof chisq tail prob
000 0 11 5.274 0.917182 0.493 0.422 0.084
001 1 12 16.864 0.154795 0.501 0.499 0.000

Ukraine_Eneolithic

left pops:
Steppe_EMBA
EHG
CHG
Ukraine_Eneolithic

best coefficients: 0.417 0.392 0.191
std. errors: 0.022 0.025 0.037

fixed pat wt dof chisq tail prob
000 0 11 18.343 0.0739553 0.417 0.392 0.191

Globular Amphora

left pops:
Steppe_EMBA
EHG
CHG
Globular_Amphora

best coefficients: 0.492 0.406 0.101
std. errors: 0.015 0.022 0.018

fixed pat wt dof chisq tail prob
000 0 11 13.246 0.277562 0.492 0.406 0.101

The best fit here is Trypillian farmers.

Folker said...

@Matt
True.
ST14 gives around 40% for Yamnaya samples, and EHG+WHG is often a bit more than 50%

@Dave
Yes, and also more Trypillia samples, and from around the Dniepr, where the contacts between early Steppe groups are attested.

And Ukraine Neolithic are also likely too old to be a direct source.

But it probably means that a part of Farmers admixture in Yamnaya is from CT, which is far more consistent than GAC.

To Samuel, it means that some of the alleles he looked at could have been selected in the Yamnaya population without been introduced by other admixture events. The Steppe admixture is not linked everywhere with BBs or Sintashta.

It could only improve his text to deal with this possibility.

Davidski said...

Since Yamnaya is generally regarded to be a fusion of Repin, Khvalynsk and Sredny Stog, it's likely that the European MN farmer admixture rich in WHG was mediated to Yamnaya via Sredny Stog. More samples from the Eneolithic North Pontic steppe are needed to test this.

Davidski said...

@All

Coordinates in all of the Global25 datasheets have been updated or added for the following samples.

Damgaard_new_scaled

Samuel Andrews said...

Folker, the origins of farmer/steppe mix in beaker and sintashta is still a mystery. I'm not pushing globular is THE farmer source. I think they are one.

At least in G25, the farmer ancestry in Beaker & sintashta looks really similar. Also it is probably at least 40% whg.

AWood said...

I'm quite sure one of the more recent L23(xL51) men from BB Hungary was also red haired, and he is also heavily steppe shifted. I'd recommend using the term "common" or "frequent" rather than popular, as that term denotes the implication of choice.

Folker said...

@Chad
You are using Steppe EMBA. I don't think it is the same as using Yamnaya Samara as Steppe MBA had additionnal farmers admixture, not necessarily from the same origin. So the results could be different. (but thx for your post)

Yamnaya did probably have both Ukraine_Eneolithic and CT admixture (through Sredny Stog/Ukraine_Eneolithic and directly). In all likehood, we don't have samples from all the right populations to find the correct mixt.

@Sam
I'm agree (and I found your paper good).
But the subject of milk has been adressed recently concerning Yamnaya:
https://hal.inria.fr/hal-01667476/file/GarnierSagartSagot_milk.pdf

They are considering that dairying could be a key element to understand the success of Yamnaya (with a datation around 2800 of the diffusion of vocabulary related to milk). Hence my remark, because clearly, rs4988235 was not frequent among Yamnaya.

Grey said...

Eric Wilds said...
"So what is the geographic demarcation that divides WHG from EHG?"

pure guess but i think the cline will eventually turn out to be somehow related to distance from the sea (as a proxy for iodine or similar oceanic rainfall nutrient) with WHG in a roughly L shaped zone closer to the Atlantic/Med and EHG more in the interior

epoch said...

@Folker & Chad

I was the one in that thread suggesting the following archaeological route could be made. At Michailovka, a site downstream of Sredny Stog on the Dnieper, the first layer of the Eneolithic was clearly related to Trypillia. Considering that the bulk of Neolithic Ukraine was found quite nearby I thought that it would be more than feasible that a Trypillian outpost would have a high local HG admixture. Think CAG or Blaätterhöhle. Later the Michailovka site was associated to Repin IIRC.

The earliest layer, Michailovka I, showed signs of cattle and sheep. Both in animal remains and fat remains analysis.

Also considering Neolithic Ukraine had a lot of I2a2a1b1 and we find that later in steppe related burials.

But OK, the modeling has some issue we now find. Anyway, Angle is going to play around a bit more he said on AG.

Ryan said...

By the way David - I realize this is off topic, but I just wanted to thank you for your help with my family's ancestry. Turns out my donor is 100% Irish so your Global 10 run called things correctly.

Matt said...

Re: Yamnaya models again, using Fst+PCoA with large numbers of Steppe_EMBA derived samples, finds that simple models of CHG+EHG, and even a more sophisticated models like this solid one by Davidski, (https://drive.google.com/file/d/12liYcpnKDLhcck5UOz3g4iH3Sv6yuT43/view), look to lack the right position in dimensions that emerge early on where steppe derived populations have very specific positions.

For instance, see: https://i.imgur.com/emUZPpG.png

I can generate a prediction of where populations would have to sit in order to admix with Ukraine Eneolithic / Trypillia to form Yamnaya: https://i.imgur.com/z9mmyH0.png

Hopefully the samples from the North Caucasus piedmont steppe eneolithic will have the right position when run through this method.

Folker said...

@Matt
North Caucasus Eneolithic is unlikely to be an answer: Wang et al. have excluded the possibility of Caucasus Eneolithic admixture in Yamnaya with formal stats (except "subtle gene-flow").

And Maykop Steppe were mainly Steppe Eneolithic with some South Siberian admixture (not shared with Yamnaya).

The admixture event between Steppe Eneolithic and Yamnaya is something very similar to GAC, so Anatolian_N + WHG, and intervened between around 3800 and 3400. Unlikely to be found near North Caucasus.

Chad Rohlfsen said...

Folker,

Steppe EMBA is Yamnaya and Afanasievo.

Folker said...

@Chad
my bad, I didn't verify before posting (I'm usually at work, so it's difficult). Your are right Afanasievo and Yamnaya are similar. I was thinking it included also Andronovo which is another story.

Jack Johnson said...

Is the south Siberian related component in steppe Maykop related to Ancient North Eurasians? I saw this component described as being related to the Kennewick man somewhere. I wonder if Q1a is tied to this since both North and East Europeans have some Q1a2 like Native Americans.

Matt said...

@Folker, the term I am using "North Caucasus piedmonte steppe" is the term used in the paper as synonymous with "Eneolithic Steppe".

Excerpted figures and text from paper- https://imgur.com/a/pX4rtNA

The "Eneolithic Steppe" samples are sampled from the foothills of the North Caucasus, not the desert steppe or herb-grass steppe to the north.

"Eneolithic Steppe" in this paper actually from a lower latitude (located more south) than "Eneolithic Caucasus", so close to the Caucasus are these samples.

But fully formed enough that they may be able to admix with Ukraine_Eneo / Trypilla / GAC to generate Yamnaya. Possibly no need for any steppe continuity outside contributions from "Eneolithic Steppe" from North Caucasus foothills. Replacement of mesolithic EHG population across virtually all of Pontic-Caspian steppe by North Caucasus piedmonte steppe eneolithic groups may have been absolute, with no local continuity.

(This is neat because "Eneolithic Steppe" + GAC / Trypilla can probably explain Yamnaya with no more geneflow from southern sources. Alternatively, if you use Khvalynsk as ancestor to Yamnaya, and there's some EHG continuity, you probably need further geneflow from CHG, which is difficult to sustain, at least in combination with geneflow from "Old Europe" because of rich Anatolian related ancestry in all Caucasus from Eneolithic onwards.)

Davidski said...

@Matt

Yamnaya doesn't come from that far south. It's archaeologically derived from Repin, Khvalynsk, and Sredny Stog.

So you're making a big call there based on three related samples that may not even be native to where they were sampled.

Matt said...

@Davidski, yeah, I understand that this is what the archaeological heads on here normally report, and to a degree that must be respected.

But genetically it seems like you don't need any other input. I don't see how Repin, Khvalysnk and Sredny Stog can work unless Repin turns out to be heavily CHG beyond either Khvalysnk or the piedmont steppe Eneolithic (just not enough CHG, esp. if not using the Eneolithic Caucasus cultures with their heavy Anatolian to top it up, as CHG proper seem long gone), or the Khvalynsk samples so far are unrepresentative and they turn out to be basically piedmont steppe Eneolithic.

As to whether the piedmont steppe Eneolithic were native to their area, well, they're the earliest samples to that region. Maybe they were, maybe they weren't. But there's no evidence at the moment that any heavily CHG population was about and moving to the north to mix with EHG. Instead genetically all populations on steppe look like mostly derived from piedmont steppe Eneolithic, in the case of Yamnaya cultures apparently without any further contribution from EHG.

Davidski said...

@Matt

Keep in mind that the Khvalynsk samples we have are from Samara, which is way up north, and one already shows a lot of CHG.

There's a lot of land between Samara in the north and Progress in the Piedmont Steppe.

Apart from that, what is important here is not the location in terms of latitude but the genetic cluster. Eneolithic Steppe is much more similar to Khvalynsk in terms of its genetic components than to Eneolithic Caucasus.

Eneolithic Steppe and Eneolithic Caucasus are like two different worlds, especially considering that they're from sites right next to each other.

Matt said...

@Davidski, yes, but as it looks all Khvalynsk show less CHG than average of Piedmont Steppe, and I don't believe any show more CHG than can be explained by being almost totally Piedmont Steppe Eneolithic.

In the absence of any heavily CHG samples about in the relevant timeframes (all Caucasus populations have Anatolia ancestry which is absent at Khvalynsk), seems the variation with Khvalynsk samples may hide much larger contributions from Piedmont Steppe Eneolithic who seem to be only population about with purely CHG ancestry.

(Khvalynsk as rather than mostly Samara HG with some small, variable CHG rather varying from less than half Piedmont Steppe Eneolithic to more than half Piedmont Steppe Eneolithic?).

Anyway we won't know til the samples can be fully analysed.
For all that, also would say there are some interesting models in the supplements that suggest that the Piedmont Eneolithic / Steppe Eneolithic formed from a mix of a Basal Eurasian population (or more likely, heavily but not absolutely Basal Eurasian population?) in common with CHG mixing with EHG directly, rather than with CHG+EHG mixture (CHG has UHG from a different source).

https://imgur.com/a/rHQgFBQ

May not be ultimately true (qpGraph can give many different viable results as we know), but if so suggests Piedmont Eneolithic may not be forming from EHG+CHG admixture, and may be divergent from both going back further in time. Possibly would suggest that why Yamnaya maybe seems to converge more with EHG relative to CHG than a population with its level of Basal Eurasian and simple EHG+CHG ancestry should seem to?

Davidski said...

@Matt

I can't say more about those samples until I've had a look at them, but I doubt that this family was native to the Piedmont region, considering how different they are from the Eneolithic Caucasus cluster. It's likely that groups with similar ratios of EHG and CHG will be found at other sites between the Black and Caspian Seas.

Samuel Andrews said...

Beaker R1b P312+ is almost intermediate between Yamnaya and Globular in pigment alleles. Bt Sintashta is nearlly fixated for G allele in rs16891982. That cannot only be explained by Globular Amphora admixture let alone only 30% Globular-like admixture. Either, R1a M417 Steppe populations were more fair than Yamnaya or there was intense natural selection that shifted frequencies shortly after admixture with farmers (which is what happened in Baltic BA for Lactose allele and pigment alleles).

Another thing. Red hair allele frequencies are almost x10 higher in modern British/Irish than in Beaker/CA Britain. Throughout northern Europe, including Baltic region & Finland, red hair allele frequencies may have gone up a lot after 2000 BC.



Open Genomes said...

@Samuel Andrews @Davidski

Do you have any explanation as to why the "European / South Asian - Steppe" lactase persistence allele rs4988235=A / I3910-T is found among the Fulani of the Sahel in Africa at frequencies from 21% to 39%?

Allele Frequency For Polymorphic Site: intron 13 C/T (-13910 ) SNP

Some other frequencies:
Hausa n=36 13.9%
Hausa n=78 2.6%
Ibo n=96 2.1%
Japanese n=98 1.0%
Hakka n=82 2.4%
Yakut n=102 7.8%

These groups are totally lacking in steppe ancestry. However, Fulani and Hausa and others in Nigeria and Cameroon have substantial percentages of R1b1c-V88, and Japanese in fact have R1b1a1a1-M278. As we know, both of these were found among Eastern Hunter-Gatherers.

Did rs4988235=A / I3910-T actually start to spread with R1, rather than strictly speaking with Eneolithic and Bronze Age steppe people?

Davidski said...

@Open Genomes

I3910-T probably initially spread with farmers from the Balkans and surrounds, and from there it made it onto the steppe and into Iberia. From Iberia it went into Africa, probably along with R1b-V88.

Global distributions of lactase persistence alleles (Liebert et al. 2017)

So yes, you're probably right, but that doesn't mean Samuel's explanation is wrong, it's just lacking some details.

Ric Hern said...

I think we have to remember that Lactase Persistence is above all connected to an infants ability to drink Mothers Milk for a longer period if I remember correctly. So the use of Dairy products from domesticated animals are secondary....

Folker said...

@Matt
You are forgetting that Damgaard et al. has concluded that the non-EHG admixture in Yamnaya is not CHG but a related population which diverged from Kotias between 20 and 27kya. Even if they missed the European Farmers ancestry, which probably explain an older split, the result is confirmed by Wang et al.
Other point, you are missing the Dolmen Cultures samples. They were able to extract enough DNA only from a LBA sample, but nevertheless he can be successfully modelized as a 2-ways Admixture CHG+Anatolia_ChL. it is meaning that a population very rich in CHG or CHG-like existed in North Caucasus at least since the mid-IVth millennia, in close proximity with Steppe Groups.
Another point: if Caucasus Steppe Eneolithic replaced all other Steppe Groups, you would have a huge founder effect on Y chromosome, with a near uniformity in Yamnaya. But we can see several founder effects related to the Steppe. And at least one with an Y haplogroup found in Ukraine Neolithic I2a S12195. So an homogeneization between the different groups present in the Steppe is more parsimonious.

Ric Hern said...

Maybe colder climates favoured the Lactase Persistence because women would have spent less time outdoors during longer Winters especially with their infants...?

The domesticated animal products could have been the boost this allele needed to become more prominent.

Ric Hern said...

Cattle were domesticated before the spread of Agriculture into Europe. Maybe R1b(V88) had something to do with it during the Late Mesolithic transition in Eastern Anatolia ? The sporadic dryer periods in the Levant most probably left wide open spaces through which R1b (V88) could have migrated into Egypt and beyond...Some R1b (V88) could have been pushed back into the Balkans and beyond by the Agriculturalists...

idurar said...

In North Africa, Berbers have steppes ancestry as well as the "European" (and other) LP alleles (I do) and some of the "European" depigmentation alleles, so that could partially explain the presence in Sub-Saharan Fulanis which can be modeled as having significant Berber-like ancestry. But not in Chadic populations like the Hausas which are much less Eurasian-shifted.
R1b-M269 is a very minor haplogroup in modern Berbers but much more common than V88, so that would go well with the picture depicted here (even though some of it is of more recent origin).
However, a more complex story is possible, with maybe V88 as a first wave of I3910-T and later (from the Bronze age on) with R1b-M269 and this time restricted to the North of the Sahara.

Ric Hern said...

Did those Northwestern African samples show the presence of Lactase Persistence ? Maybe it entered Africa via two different routes ? One through Egypt and the other mostly later through Iberia during Celtic and Germanic Migrations ?

Matt said...

@Davidski, pretty doubtful we can describe these individuals as a family; at the very least you've got two sites at Vonyuchka 1 and Progress 2, and the two individuals at Progress 2 are at separated graves, don't share mtdna or y-dna, aren't detected as relatives based on autosome.

They're at least likely to represent the general population of the piedmont steppe region, even if that population formed recently to their dates, not reflect the admixture history of one family which has had an atypical contribution of a far flung source for its location.

@Samuel, question is whether this sample (I6561) has higher ratio of CHG:EHG than can be explained by Steppe_Eneolithic (North Caucasus piedmont steppe Eneolithic). If not, then not evidence for heavily CHG populations about.

@Folker, Yamnaya by the MOMI based method having ancestry from a population that diverged from CHG at a relatively old date is not inconsistent with the piedmont steppe eneolithic being a long separated population and not a relatively recent admixture of CHG+EHG. In fact it actually supports it if anything.

Re: Dolmen LBA, that qpAdm result is likely to be wrong.

The supplements shows that Dolmen LBA has no difference in outgroup f3 sharing with Anatolia relative to any of the post-eneolithic Caucasus populations, nor f4 stats, and nor does ADMIXTURE or the PCA give it a special position similar to CHG. It's not a CHG survivor in any measure other than a qpAdm which I have serious doubts about the ability to separate the populations in question in any meaningful way.

See here for the specific figures:

I'm not forgetting Dolmen_LBA, it's when you read the rest of the paper, the evidence for it "saving" the idea of a late CHG rich survivor population that was neither Piedmonte steppe Eneolithic (very rich in EHG related ancestry, enough that contribution from other EHG would have to be minimal in Yamnaya) or Caucasus Eneolithic (rich in Anatolian ancestry, so a bad potential ancestry for Yamnaya), that evidence is just not there in any of the simple, transparent measures in the paper.

Re: y, we have no idea how diverse the piedmont steppe eneolithic was on the y yet (assuming that they were a stable population). There is no reason to assume they had a single haplogroup, or that they were uniform, so no reason to assume any descendant population was. As well, at least likely that some other y came in via Globular Amphora / Trypillian / Ukraine Eneo ancestry path.

Davidski said...

@Matt

OK, I must have got them mixed up with another batch of relatives.

In any case, my point was that there's no reason to take the average EHG/CHG ratios of Eneolithic Steppe on one hand, and Khvalynsk on the other, and assume that there was a gradual cline from the Piedmont Steppe in the south to Samara in the north in terms of these ratios.

There aren't enough data points to do this, with a massive gap in space and time of a couple thousand miles and years.

I'd be very surprised if the Khvalynsk outlier with heavy CHG or the Sredny Stog II R1a-M417 guy, also with a lot of CHG, came from the Piedmont steppe. My bet is that they came from somewhere in between the Caucasus and Samara.

Folker said...

@matt
Dolmen Culture LBA is one of the population which could be the result of a 2-ways admixture. It was tested with qpwave. All others are at least a 3 ways admixture.
Not a coincidence if you could modelize him as a 2-ways admixture between CHG and Anatolia_ChL. It is also consistant with archeology, as D.C. is not related to Maykop and is quite mysterious. I also don't think that ADMIXTURE or a PCA can say anything precise about the exact number of admixture events which happened to form a population.
By the way, it is perfectly possible from an archeological point of view, that different populations coexisted in the Caucasus. With various influences from the South and from the East.
By the way, your point about I2a is not very convincing. And what if the P312 rumor in Khvalynsk is confirmed?

Folker said...

Again, I was writing from my phone, without access to the paper.
So, to be precise, they tested different propositions with qpWave for the Caucasus Cluster. In Sup Table 5, we have the result for 1 stream of ancestry, and the proposition was not rejected only for Eneolithic Caucasus and Dolmen LBA. In Sup Tab 6, we have the results for 2 streams of ancestry, and the proposition is not rejected in any case.
So, it does mean that Dolmen_LBA is likely not the result of recent admixture. And a 2-streams admixture is only possible between a CHG-rich population and and Anatolian_N derived population.
This is backing the idea that some populations CHG-rich were present very late in the Caucasus. Dolmen Culture is dated from the mid-IVth millenia, and if the lone LBA sample we have doesn't show much trace of recent admixture, it could mean that the admixture event could be dated from the beginning of the Dolmen Culture, or before. Difficult to say more, without more samples. Too bad that the EBA samples were too partial.
In any case, it means we can't rule out the possibility that some CHG-rich populations still existed in the Vth and the IVth millenium.
Remember that North Caucasus doesn't show trace of migration from the South during Neolithic. There is continuity in lithic industries between Mesolithic and Neolithic (but big changes after).

Open Genomes said...

@Samuel Andrews @Davidski

rs12913832=G is found among populations worldwide, from West Africa, to East Africa, to Southeast Asia, to Siberia, to unadmixed Native Americans. *I didn't include Austrialian Aboriginals, who might be admixed, but they too have very high frequencies.) This doesn't appear to be at all related to Steppe or European ancestry!

In particular rs12913832=G reaches very high frequencies among the Samaritans and the Karitiana and Surui, who have no Steppe ancestry whatsoever.

ALFRED Allele Frequency For Polymorphic Site: rs12913832=G

rs12913832=G is found among the following populations
Malinke (aka Mandinka) n=226 2.2%
Amhara n=44 2.9%
Ethiopian Jews n=72 5.6%
Ethiopian Jews n=62 6.5%
Masai n=286 0.3%
Masai n=38 2.6%
Masai n=34 2.9%
Zaramo (Tanzania) n=78 1.3%
Mozabites n=60 10.0%
Mozabites n=52 9.6%
Bedouin n=98 9.0%
Bedouin n=96 10.0%
Bedouin n=90 11.1%
Chaldeans n=44 20.5%
Druze n=90 32.0%
Druze n=94 34.0%
Druze n=84 32.1%
Druze n=200 36.5%
Jews, Yemenite n=80 16.2%
Jews, Yemenite n=74 13.5%
Samaritans n=76 48.7%
Hmong n=66 3.0%
Khamba Tibetans n=68 5.9%
Tibetan n=200 0.5%
Tibetan n=92 1.1%
Tibetan n=50 20.0%
Xibe n=58 3.4%
Cambodians, Khmer n=20 30.0%
Cambodians, Khmer n=18 5.6%
Cambodians, Khmer n=46 2.2%
Cambodians, Khmer n=30 3.3%
Thai n=1024 0.6%
Thai n=406 0.5%
Thai n=188 1.1%
Timorese n=234 2.2%
Chukchi n=44 6.8%
Yakut n=50 12.0%
Yakut n=50 4.0%
Yakut n=100 9.0%
Yakut n=42 11.9%
Cheyenne n=110 4.6%
Yavapai n=124 3.2%
Yupik (Inuit) n=44 13.6%
Maya Yucatan n=50 10.0%
Karitiana n=48 29.0%
Karitiana n=110 25.5%
Karitiana n=26 30.8%
Karitiana n=50 24.0%
Surui n=42 19.0%
Surui n=42 21.0%
Surui n=84 15.5%
Surui n=46 10.9%

Matt said...

Davidski: In any case, my point was that there's no reason to take the average EHG/CHG ratios of Eneolithic Steppe on one hand, and Khvalynsk on the other, and assume that there was a gradual cline from the Piedmont Steppe in the south to Samara in the north in terms of these ratios.

Hmmm. That's a more solid point than I thought and I didn't consider it. The Steppe Eneolithic / Piedmont Eneolithic genotype may have extended a bit north of the Piedmont, even if it *was* long standing in the Piedmont, and we haven't enough evidence on that yet.

Though I wouldn't be surprised if it was pretty specific to the piedmont though - there seems like a lot in the archaeology about quite thin occupation of the steppes to the north of piedmont limited to river valleys which changed in a big way with development of wagons. So I wouldn't be too surprised if it turned out that groups from the piedmont were able to expand in a big way once that technology was developed. Pottery types seems like the main evidence for cultural continuity, but those can be misleading as it seems like migrants have often adopt new pottery styles on the move (this disguised the migration signal in Corded Ware for some archaeologists).

Open Genomes said...

@Samuel Andrews @Davidski

Plantinga et al. (2012) Low prevalence of lactase persistence in Neolithic South-West Europe

In this study, we have investigated lactase persistence of 26 out of 46 individuals from Late Neolithic through analysis of ancient South-West European DNA samples, obtained from two burials in the Basque Country originating from 5000 to 4500 YBP. This investigation revealed that these populations had an average frequency of lactase persistence of 27%, much lower than in the modern Basque population.

I wouldn't exactly call a frequency of 27% in Iberian Chalcolithic samples "low", except in relation to today.

In this study, we have analysed 46 samples that are derived from human teeth from burials originating from the Late Neolithic–Chalcolithic era in the North of the Iberian Peninsula. Previously, these samples yielded reproducible human mitochondrial DNA sequences and were extracted from intact well-preserved teeth.

For the amplification of the promoter region of the LCT gene several primer pairs have been developed and initially tested on modern DNA for their specificity and PCR efficacy. On the basis of these observations, three primer pairs were chosen to use in the PCR amplifications of the ancient DNA (Table 1). In total, 26 ancient DNA samples could be analysed for the LCT −13910 genotype, hence a PCR efficiency of 57%, which revealed an average lactase persistence frequency of 27% (Table 3). Furthermore, mtDNA HVR-I haplotypes of the ancient DNA samples have been generated, as depicted in Supplementary Table 1. Calculation of the SD from frequency estimates was performed after excluding samples that have identical genotypes for both lactase −13910 and for mtDNA HVR-I and originate from the same burial to correct for possible consanguinity. On the basis of these criteria, four samples had to be excluded. With the exclusion of these samples, the calculation revealed 2 × SD=0.12 and lactase persistence frequency is 0.27 with 95% CI 0.15–0.39.

Davidski said...

@Matt

This discussion reminds me of the one we had about the five Armenia Chalcolithic samples and how they fit into this picture.

I'm pretty sure that Ukraine Eneolithic/Sredny Stog II I6561 doesn't have much directly to do with the Piedmont Steppe.

He's dated to 4045-3974 calBCE and already looks significantly "Yamnaya".

Davidski said...

@Open Genomes

That Spanish study is based on PCR results. Let's see them reproduce their 27% with UDG-treated capture data.

Open Genomes said...

@Samuel Andrews @Davidski

SLC45A2 Leu374Phe rs16891982=G is found in both the Levant Neolithic and Anatolian Neolithic. Both of these populations are lacking in CHG.

I1707 Levant PPNB 7722–7541 BC 1/1
I0867 Levant PPNB 7300–6750 BC 4/9
Tep006 Pottery Neolithic 7500–5800 1/1

Asia Minor Neolithic I0723 1/2
Asia Minor Neolithic I0736 8/14
Asia Minor Neolithic I0744 3/6
Asia Minor Neolithic I1096 19/19
Asia Minor Neolithic I1100 1/3
Asia Minor Neolithic I1102 2/2
Asia Minor Neolithic I1103 3/5
Asia Minor Neolithic I1579 10/10
Asia Minor Neolithic I1580 5/5
Asia Minor Neolithic I1585 13/13

In modern populations, many groups without any Steppe or CHG ancestry carry rs16891982=G:

ALFRED Allele Frequency For Polymorphic Site: Leu374Phe (rs16891982=G)

Among others:
Malinke (Mandinka) n=226 0.4%
Mende n=170 1.2%
Yoruba n=176 0.6%
Luhya n=134 1.5%
Luhya n=194 1.0%
Luhya n=198 0.5%
Evenki n=68 14.7%
Japanese n=48 4.0%
Japanese n=56 10.7%
Japanese n=178 0.6%
Tibetan n=200 1.5%
Tibetan n=100 1.0%
Tibetan n=126 0.8%
Tibetan n=50 30.0%
Yi n=20 5.0%
Cambodians, Khmer n=18 5.6%
Hakka n=100 1.0%
Thai n=1024 0.5%
Thai n=406 0.2%
Thai n=188 1.6%
Surui n=84 2.4%

Samuel Andrews said...

@OpenGenomes,

Btw, I'm pretty sure some of ALFRED results are inaccurate. rs16891982=G existed in basically all of Europe, except western Europe, and much of Middle East starting since at last the Mesolithic. I agree it long predates the Yamnaya expansions.

What I show in the post, is its frequencies get really high aftr Yamnyaa-related expanisons. I think this is because Steppe groups mixed with eastern European farmers like Globular Amphora (who might have been fixated for the allele like modern EUropeans) then spread the pigmentation genes of these farmers across Europe alongside Steppe ancestry.

Samuel Andrews said...

@Open Genomes,

Of course rs12913832=G exists in Asia and a few spots in Africa. I don't claim this allele originated in LNBA Europe. I claim, the high frequencies seen in modern northern Europeans, derives from LNBA Steppe-rich movements that picked up high frequencies from eastern European farmers.

Open Genomes said...

@David

Can you provide the unscaled sheet for Daamgard (2018)?
This for doing the scaling on the fly. Thanks.

Davidski said...

@Open Genomes

https://drive.google.com/file/d/1Dj8ysMY4oePcbW5PszuiCnDBJi9ANjtt/view?usp=sharing

Creative said...

I'm kind of curious if it is possible to pinpoint a male source population from whom especially Central Europeans, inherited early forms of balding “Male pattern hair loss”.