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Monday, October 20, 2014

Analysis of Hinxton4 - ERS389798


Hinxton4, or ERS389798, is one of five ancient English genomes stored at the Sequence Read Archive under accession number ERP003900. However, this analysis is based on the genotype file of Hinxton4 available at Genetic Genealogy Tools. For more information and some speculation about these genomes see my earlier blog post here.

I still don't know who these samples represent exactly, but in all likelihood, this is one of the two Iron Age sequences from the collection, and probably belongs to a Briton of Celtic stock. Note, for instance, its high affinity to the present-day Irish, relatively low North Sea score in the Eurogenes K15, and pronounced western shift on the second Principal Component Analysis (PCA) plot below.

Interestingly, Lithuanians top its shared drift list based on the Human Origins dataset and more than 360K SNPs. I'm not entirely sure what this means, but it's probably related in some way to the unusually high level (>45%) of indigenous European hunter-gatherer ancestry carried by Lithuanians.



Shared drift stats of the form f3(Mbuti;Hinxton4,Test) - Eurogenes dataset

Shared drift stats of the form f3(Mbuti;Hinxton4,Test) - Human Origins dataset



Eurogenes K15 4 Ancestors Oracle results

See also...

Analysis of Hinxton2 - ERS389796

Analysis of Hinxton3 - ERS389797

Analysis of Hinxton5 - ERS389799

Hinxton ancient genomes roundup

107 comments:

Davidski said...

By the way, I tested the level of Early European Farmer (EEF) admixture in Hinxtons 2, 3 and 4, using the following equation:

f4(Mbuti, Ami; Loschbour, Test) / f4(Mbuti,Ami; Loschbour, Stuttgart)

This is very similar to what was done in Laz et al. 2014, and here's what I got:

Hinxton2 - 0.434633

Hinxton3 - 0.492412

Hinxton4 - 0.515643

I can't test WHG or ANE in this way, unfortunately.

Chad Rohlfsen said...

Interesting. I would still guess 45%, with him plotting by the Irish/West Scottish.

Chad Rohlfsen said...

I'd be interested to see how my results change, with this method. Thanks, for all the work David. Do you know what times specifically the Samara, Corded Ware, and other talks are?

Ryan said...

Could the shared drift be a Proto-Indo-European signal?

Chad Rohlfsen said...

Razib Khan ‏@razibkhan · 1m1 minute ago
#ASHG14 eastern hg from Karelia and sammara. ANE related to Eastern hg. yamnaya had near East and Caucasus

BAM!

Chad Rohlfsen said...


ASHG14 yamnaya better source for intrusive group into north Europe late Neolithic bronze age


Details


Razib Khan ‏@razibkhan · 1m1 minute ago
#ASHG14 corded ware 36% nonlocal ancestry. Karelian. low bound


Chad Rohlfsen said...

#ASHG14 yamnaya modeled as 50/50 Armenian Karelian. corded ware 75% yamnaya

Chad Rohlfsen said...

#ASHG14 yamnaya % peaks in north Europe. lower in south Europe. lowest in Sardinia

Chad Rohlfsen said...

#ASHG14 yamnaya = proto-indoeuropeans

#ASHG14 south Asia hard to model. no ancient dna

#ASHG14 re%3A Y chr will be included in new paper

Chad Rohlfsen said...

#ASHG14 corded ware localized to center north Europe. not clear if ANE west Europe due to later migrations

Chad Rohlfsen said...

#ASHG14 3 anglosaxons 2 iron age celts

#ASHG14 old samples cluster sort of with modern British. anglosaxon Finn shifted iron age Spain shiftef

#ASHG14 modern British more rare variant with Spanish affinity vs Finn. Anglo Saxon more with Finn. Iron Age more affinity Spanish

Chad Rohlfsen said...

#ASHG14 Cornwall less Finnish. Saxon cline

#ASHG14 rare variant counts excellent information tree building

#ASHG14 Britain Finland diverges 6k BP. iron age clusters with modern Britains anglosaxon different. sounds like little German pop movement

SS: Anglo Saxon samples have ancestry from northern Continental Europe, consistent with early migration #ASHG14
Schiffels: older Iron age samples more like present British samples, while younger AS samples left little imprint on modern GBR. #ASHG14
BAM! Again!

Chad Rohlfsen said...

No Saxon replacement.. modern Brits are more like the Iron Age samples.

Chad Rohlfsen said...

#ASHG14 first cluster break Finns break out rest of Europe. then Scandinavian. then Ireland. then north vs south Europe


#ASHG14 sw Germany vs east Germany. national boundaries are real!

Leslie: fineSTRUCTURE analysis of haplotypes from 515k SNPs in 6209 Europeans: 150 unique clusters #ASHG14

#ASHG14 southern France Spain transnational boundary Catalan/provence. lang de oc

Leslie: Southern France and Spanish (Barcelona) clusters. Norway has a lot of sub-clusters. #ASHG14


#ASHG14 northern France more like Germany than Italy. think old Celtic affinity not franks (razib opinion last)


Chad Rohlfsen said...

#ASHG14 Brittany shares nontrivial with Irish. Celtic migration

Quick pop into human population session just in time to see that Danes are more similar to Germans that to other Viking nations #ASHG14

#ASHG14 v
novembre on Sardinia

#ASHG14 Sardinia has a lot of early Neolithic ancestry (not much bronze age stuff)

#ASHG14 sikora 2014 good map of admixture history

#ASHG14 sampling in ogliastra mountainous region in Sardinia. 3500 4x coverage

Novembre: Arzana village from Lanusei valley has high differentiation from rest of Europe by Fst and f2-haplotype lengths. #ASHG14

Chad Rohlfsen said...

Novembre: , PC1 vs. PC2 = horseshoe shape from N. Afr. to Middle East to N. Eur, suggesting Mediterranean is a barrier. #ASHG14

#ASHG14 effective migration surface migration rate between demes

#ASHG14 two models. Sardinia recent divergence & rapid drift. vs old divergence

Chad Rohlfsen said...

Novembre: , PC1 vs. PC2 = horseshoe shape from N. Afr. to Middle East to N. Eur, suggesting Mediterranean is a barrier. #ASHG14

#ASHG14 effective migration surface migration rate between demes

#ASHG14 two models. Sardinia recent divergence & rapid drift. vs old divergence

Chad Rohlfsen said...

From what I gather, corded ware was 36% Armenian/Karelian like. So maybe 20- 25% ANE? I bet bell beaker will be pretty similar.

Chad Rohlfsen said...

Sorry to gloat, but I was right about the Caucasus.

Chad Rohlfsen said...

And the make up of indo Europeans, being more farmer than anything. Maybe, 50% EEF, maybe 25% WHG, 25% ANE.

Davidski said...

Describing Yamnaya as Armenian/Karelian seems like a way to place them in present-day Russia. It doesn't mean they actually were Armenian/Karelian, just like modern Europeans aren't actually Sardinian/Karitiana, even though they can be modeled as such.

Chad Rohlfsen said...

Armenians are at least 82%EEF/Near Eastern. Karelians can be 15-20% So one would gather from that it should be around 50%EEF. The EEF source is Caucasus, so it could lack any WHG/UHG in it.

Chad Rohlfsen said...

Either way, they should be around 50% farmer, to be able to be crossed that way.

Chad Rohlfsen said...

I know it isn't about modern pops, but an expression. Still it is something quite farmer, mixed with something quite 'West Siberian'.

Davidski said...

Yamnaya EEF should be mostly from the Balkans, from Cucuteni-Tripolye farmers moving east, which is well documented.

Matt said...

Thanks for the tweets Chad. As I thought might be possible re the "Scratch the North Caucasus" post, the Yamanya can be modelled as a mix of slightly more Eastern (i.e. ANE shifted) hunter gatherers than Motala and South Caucasians.

(And it looks like they may have been keeping findings of models between Caucasians and Scandinavian-Baltic hunter gatherers between the lines, after all ;) ).

Be interesting to see if they have any specific evidence that that's what happened or if this is just an approximation they've gone with because the Karelia sample and Armenians allows them to fit Yamnaya that way.

The alternative is the earlier idea about a more simple mix between EEF and an unknown population with higher ANE:WHG ratio than Baltic hunter gatherers, could still stand, just that Yamnaya was already EEF mixed.

But modelling Yamnaya without EEF and instead Armenian means that we can use the hunter gatherers we have, rather than postulate ones that we don't have any evidence (or at least evidence for at this point in history).

Either way, what we know concretely is the Yamnaya culture (these samples) has Early Neolithic (Near East) levels to a degree consistent with being around 50% Armenian 50% Baltic Hunter Gatherer. Probably about a third "Near East" overall we could say?

Incidentally this would suggest that Lithuanians are not too far away from where Yamnaya would've been. So maybe Northwest Europe (Germany, Great Britain) is around 2/3 Yamnaya 1/3 Early Farmer and Spanish 1/3 Yamnaya and 2/3 Early Farmer. The Baltic languages are the most "archaic" and least derived apparently of the Indo-European languages, looks like that perhaps may be due to a relatively low substrate effect.

It's a puzzler about those comments that the Iron Age sort of clusters with modern Brits closer with Anglo Saxon age samples. Of course, that's basically what it looks like from Davidski's analysis (gratifying supports that his treatment of the data is correct), but the paper's abstract mentioned that "the Anglo-Saxon samples resemble more closely the modern British population than the earlier samples". Maybe some pre conference revision?

Chad Rohlfsen said...

Lazaridis said they had Near East and Caucasus.

I'm not trusting anything other than the DNA. Schiffels just showed that Saxon input is much less than native ancestry, in Britain. Sometimes sources aren't as good as data.

Yes Matt, it looks like revision on the British part. Anglo-Saxon input is minimal, apparently.

Chad Rohlfsen said...

Matt,
I still think it could be 50% EEF. Armenians have too much EEF, to be modeled in the Laz way, and Karelians have some EEF. Probably under 60%EEF, but definitely over the Lithuanian 32% or whatever they are.

ZeGrammarNazi said...

Given that Anatolian is considered by some linguists to be a sister language to PIE and not a descendant, the Yamnaya people can be modeled as 50% Armenian, and that the abstract states that the oldest Samara Valley samples were 100% mtDNA U and that they became more diverse as time passed, I believe it is possible that a Proto-PIE language was already spoken south of the Caucasus and the mixture of migrants from the Caucasus with the steppe populations led to actual PIE which then spread across the ancient world. While PIE's sister language, Anatolian, stayed south of the Caucasus.

This might explain why we are finding oxen-pulled (probably) chariot-like wagons in the Caucasus and then actual chariots later on in Samara Valley.

Not saying this is the gospel, but just a thought I had while reading some of these tweets,

Davidski said...

There were Neolithic migrations from the Near East and Balkans into the steppe. These weren't the Indo-Europeans.

Later, there were migrations from the steppe to Anatolia, which is probably how ANE ended up there.

This fits with linguistic evidence, which puts PIE on the steppe, and Anatolian as a early split that arrived from the steppe either via the Balkans or Caucasus.

By the way, there was mtDNA H in the Samara Valley during the Mesolithic. Reich said this via e-mail.

Matt said...

@ Chad Lazaridis said they had Near East and Caucasus.

Karelians have some EEF

Yeah, one of those tweets made specific reference to the Caucasus. If so, like I say, will be interesting why they say that, whether they have specific evidence making that link.

On EEF, I have only given an estimate for what we usually call ENF, and it was a bit of a high estimate probably. If modelling Yamnaya using EEF, maybe a little higher than a third but lower than half (in addition to whatever else they have)?

Also, why would Karelians necessarily have EEF if I am reading the tweets correctly and they are described as "eastern hg from Karelia...ANE related to Eastern hg" i.e. eastern hunter gatherers from the Baltic coast. I wouldn't assume they have any Neolithic mixture necessarily.

Chad Rohlfsen said...

David,
I'm sure there is some tripolye ancestry, but probably minimal if they need Armenians to cover the farmer ancestry. I did mention the H in another hinxton section. One link is h13 in the Caucasus and Britain.

Chad Rohlfsen said...

If these Bronze Agers are 40-50% farmer, then that means we may have only had a 50% replacement during the Neolithic, for Northern Europe.

Davidski said...

I'd say Cucuteni-Tripolye farmers were like Armenians minus any ANE.

By the way, the DNA evidence is apparently consistent with linguistic evidence.

https://twitter.com/Luke__Ward/status/524255506181804032

Chad Rohlfsen said...

I wonder if this means that R1b is the group that took out the Balkans, then split into an Anatolian and Northern Europe group.

Chad Rohlfsen said...

Maybe Bell Beaker, is that 1500 year dark area of Pre-Celtic, according to Anthony. That would be close to the dates for German Beaker until Urnfield. Roughly 13-1400 years.

Chad Rohlfsen said...

Northern Europeans being 70-75% Yamnaya, do you feel it is safe to put R1b there, now that we know Northern Europeans are Yamnaya derived? The recent rapid expansion fits.

Chad Rohlfsen said...

Or probably 2/3, as Matt said.

Chad Rohlfsen said...

#ASHG14 poster from Estonian group shows massive Y chr growth bottleneck 4 to 8 K BP

#ASHG14 signals of denisovan in miao and south India (weak(

#ASHG14 khosean start divergence before out if Africa. 200k bp

#ASHG14 hsieh archaic introgression into pygmies etc.

Matt said...

I'd say Cucuteni-Tripolye farmers were like Armenians minus any ANE.

I think that's a plausible comment. Although who knows until we have adna.

But I would point out that Armenians minus any ANE seems essentially going to be like Palestinians-Bedouins, as Armenians model more or less as Palestinian-Bedouin plus ANE and WHG. Not like the "EEF" LBK farmers, who seem like they can be modelled as Bedouin-like with a fairly significant dose of WHG mixture. It might confuse matters to think of a population like this as EEF exactly.

Using either Palestinians, Bedouins or Stuttgart plus an unknown population to model Yamnaya will come to quite different conclusions about how the WHG:ANE ratio of the unknown population (and levels of mixture).

"Old Europe" is supposedly quite homogenous as a culture, so we'd wonder if Stuttgart and Cucuteni-Tripolye were significantly different in WHG levels, for all that samples like the TRB show that some fluctuation in WHG admixture is possible.

Davidski said...

Armenians are modeled as GujaratiC/Stuttgart in Table S11.1 of Laz et al. 2014.

ryukendo kendow said...

This is extremely exciting.

It seems like the connection of IEs to both Siberia/NE Europe and the Caucasus is confirmed. We have to wait for details, but this is really satisfying as many here have reached this conclusion a long time prior.

One issue: the usage of the words EEF, when one is really trying to refer to Basal Eurasian, is confusing; Armenian have very high basal, even more Basal than Sardinian or EEF, while EEF is a ~50/50 stabilized mix of WHG and Basal that is specific to Europe, and the major source of Basal in all Europeans--including Balkan pops.

The figures that are given here suggest that there is less WHG than both Basal and ANE in PIEs. Razib said: Eastern HG (ANE) away from Western HG, yamnaya toward malta; eastern HG from Karelia and Sammara; yamnaya had Near East and Caucasus(Not EEF!); yamnaya 50/50 Karelian + Armenian; Corded ware 75% yamnaya; corded ware 36% Karelian--It seems like Karelian is becoming a proxy for ANE, Armenian for Basal, with WHG only incidental in the Basal and ANE sources that contributed to PIEs.

All this cannot be produced by EEF+ANE, as would be the case should the farmer ancestry be from European farmers, because any WHG in the ANE source, when added to substantial EEF, would make WHG the largest slice of ancestry, unless EEF itself were very low, which does not appear to be the case if PIEs can be modeled as 50% Armenian. But it can be produced from a Caucasus+Siberian HG mix, as neither have very much WHG.

Davidski said...

I'm assuming when he says Malta, he actually means Mal'ta boy.

Davidski said...

rk,

Just keep in mind also, as per above, Armenians are best modeled as GujaratiC/Stuttgart when ancient genomes are used.

And they're best modeled as GujaratiD/Sardinia, when modern pops are used.

barakobama said...

Thanks alot Chad!!!

"#ASHG14 eastern hg from Karelia and sammara. ANE related to Eastern hg. yamnaya had near East and Caucasus"

Eastern hunter gatherers were from Karelia and Samara? What? Khan must have made a mistake there.

"ASHG14 yamnaya better source for intrusive group into north Europe late Neolithic bronze age"

Common sense. I wish they'd be more specific. What about Indo Europeans in southeast Europe, west Asia, and central-south Asia?

"#ASHG14 corded ware 36% nonlocal ancestry. Karelian. low bound"

"#ASHG14 yamnaya modeled as 50/50 Armenian Karelian. corded ware 75% yamnaya"

This can't be right. Karelians have a high amount of east Asian ancestry, which Yamna lacked(at least maternally). Armenians only have 14.51% ANE and East-Finnish only have 20.98%(Some is of Siberian origin), according to Davidski. This would mean Yamna had 17.745%, which is obviously wrong.

https://docs.google.com/spreadsheets/d/1v4zYizoWtsoW1MNBN7SUrLf8R62NHPbMRySUJ2J48_Q/edit#gid=1410860471

If 50% Armenian and 50% Karelian is a good fit for Yamna, they should score a little more WHG than Stuttgart in ANE K7 and around 30% or a little more ENF.

Corded ware had 36% "nonlocal"(non Neolithic-descended central European?) and 75% Yamna ancestry? Those two statements contradict each other.

"#ASHG14 yamnaya % peaks in north Europe. lower in south Europe. lowest in Sardinia"

This can be seen by looking at the distribution of ANE in Europe. But what about the ANE in west Asia, do they think it's mostly non-Yamna related? They seem convinced almost all ANE in Europe, I guess outside of the far-eastern part, descends from Indo Europeans.

R1b one way or another came from west Asia, plus plenty of the ANE in Italy and the Balkans probably came from west Asia, not Yamna.

"#ASHG14 south Asia hard to model. no ancient dna"

That's disappointing I'd think they'd be able to at least identify Yamna ancestry. They can make a general estimate without ancient DNA from South Asia.

#ASHG14 re%3A Y chr will be included in new paper"

"#ASHG14 corded ware localized to center north Europe. not clear if ANE west Europe due to later migrations"

Did they say this at the conference or did Khan add in the west Europe thing? NW Europeans have very similar amounts of ANE as NE Europeans, so it probably comes mostly from the same source.

But what about the ANE in Finno-Urgics? The same pattern of ANE exists in Finno-Urgic speaking NE Europeans.

Chad Rohlfsen said...

Guj/ sard is still plotting way away from Stuttgart. It's gotta be almost all near east, with little Balkan flow.

Matt said...

Davidski: Armenians are modeled as GujaratiC/Stuttgart in Table S11.1 of Laz et al. 2014.

Sure, and the lowest f3 pairs for Lezgins, Chechens, Cypriots, etc. was Stuttgart and MA-1.

Yet mixes of Stuttgart and MA-1 actually failed on to represent Georgians and Lezgins on their formal tree modelling (Figure S14.20).

Essentially due to Stuttgart's excess WHG - instead, models where Stuttgart was a mix of WHG (or UHG here) and Near East, and they then used Near East mixed with ANE worked to model Lezgins, etc. worked.

(Also the lowest f3 for Lithuanians was Abkhasian plus Loschbour...)

Ryukendo - we won't know until we later but I think the Karelian HGs are probably still much more (or much closer to) WHG than ANE. Motala12 has a ratio of 4:5 WHG to ANE. Karelia is not too far east of that.

BO - "This can't be right. Karelians have a high amount of east Asian ancestry"

I'm assuming the implication of the tweets was that they sampled ancient Karelian HGs, who may not have had an East Asian ancestry.

Chad Rohlfsen said...

Barak,
It's probably more like 20-25% ANE. That's is the best fit, if they are 2/3 of our genes.

Davidski said...

The Balkans during the Neolithic weren't the same as they are now.

Btw, I have no idea what Razib is saying in those tweets, and whether he's talking about modern or ancient Karelians.

He might be referring to models that use present-day Armenians, who are hardly purely Near Eastern, and Mesolithic Karelians with really high levels of ANE.

Chad Rohlfsen said...

50/25/25 is my guess...

Chad Rohlfsen said...

David, what if r1b was in west Asia, basically identical to Armenians, when it entered the steppes? Farmer genes take out most of the ANE, like the WHG in Europe. Or we have r1a and r1b on the steppes, together, r1b more south, perhaps. Either way, r1b looks very yamnaya now, if it's 2/3 of our genes, plus the 3-5kya rapid expansion.

Matt said...

@ Davidski re: Razib's tweets - As I read it, and this is only as I read it, they've got HG samples from around about where Russia is (Karelia near the White Sea and Samarra) and they've got Yamanya samples. These are all samples out of actual ancient bones.

They've then run some models where they try to model the Yamanya samples using the Samarra and Karelian HGs and other populations. These models fail with Stuttgart and succeed with Armenians, for whatever reason. (Implication -models that succeed with Stuttgart (i.e. "EEF") would require HGs that do not match the characteristics of what they actually seem to find existed in Russia at that time.)

Hopefully Razib will give us a clearer update if he can, and we will see if I am reading him right.

Chad Rohlfsen said...

Stuttgart isn't Near Eastern enough. That's my guess. Maybe they fit better as 60%+ or 40-45% Near Eastern.

barakobama said...

So was Yamna a mixture of Karelian and Samara hgs, and some type of near eastern farmer? If Karelian Hgs were lets say 30% ANE and 70% WHG, and Yamna were 50% Karelian hg and 50% Armenian, they should be around 42% WWG or slightly more(Armenians score around 14% I think, can't find the K7 spreadsheet). In terms of Laz maybe they'd be around 35% WHG. Their ANE would be under 30%, which is a huge surprise.

"Barak,
It's probably more like 20-25% ANE. That's is the best fit, if they are 2/3 of our genes"

2/3, that's hard to believe. But if Yamna was 50/50 Kar. hg and Armenian, I guess it kind of makes sense. The story of Europeans is obviously more complicated than Gok2+Yamna though. There have to be other WHG sources.

If Yamna is a big ancestral source for NW and NE Europeans, why is there such a divide between the two regions in admixtures?

Maybe ethnic groups in Russia today aren't as differnt from Yamna as we've assumed.

Chad Rohlfsen said...

Just for fun, let's say...

Karelia is 50/50 WHG/ANE

Armenians are 86% Near Eastern/ 14 ANE

We get 43% Near East/25% WHG/ 32%ANE

Chad Rohlfsen said...

Which might fit better as we have Spain, and parts of Italy, almost Southern France, (not just the Balkans) who are more ANE, than WHG.

Chad Rohlfsen said...

Barak,
It would seem that a good deal of our WHG is survival from the Neolithic. There may have been less than a 50% replacement of WHG, with EEF, if the invaders were 50% EEF, without a lot of WHG. It seems their female mtdna legacy, is stronger than what they brought.

barakobama said...

Chad,

We can only speculate about the Karelian HGs. Southern Swedish hgs were only ~19% ANE. We'd have to ask an expert on Mesolithic archaeology if Karelian HGs mostly derived from a eastern Ice age-refuge, unlike Swedish HGs. My guess is they had alot more ANE, but defiantly a decent chunk of WHG. This conference took down any theories that PIE were something like 55% ANE, and allows them to contribute alot more ancestry to Europeans than previously thought.

Khan mentioned in one of his tweets that early Neolithic and mid Neolithic were differnt. Maybe WHG rose, which can help explain current levels.

Chad Rohlfsen said...

I am being generous and making it 50/50 WHG/ANE. It may be more WHG. Yes, hunters were absorbed more and more, as the Neolithic went. They were 'hiding in the woods'. Neolithic settlements were usually small and sparse by todays standards. Plenty of room for roaming bands of hunters and fishers.

Davidski said...

Swedish hunter-gatherers were partly of Karelian stock IMO.

In other words, they were a mixture of WHG coming from the direction of Iberia and eastern hunter-gatherers moving down via Fennoscandia.

Davidski said...

Matt,

The Karelia/Stuttgart model fails while the Karelia/Armenia one succeeds probably because Armenians have around 15% ANE.

Chad Rohlfsen said...

If bell beaker is 75% yamnaya, it should be around 25% ANE too.

Matt said...

Davidski: The Karelia/Stuttgart model fails while the Karelia/Armenia one succeeds probably because Armenians have around 15% ANE.

I think that's part of it, but also because Armenians have less WHG than Stuttgart as well.

Mixing Stuttgart with Karelia would probably give a population which was too WHG relative to its ANE and Near East to fit Yamanya, if Karelia are likely predominantly WHG (and I think it's likely they are).

Modern day Armenia likely isn't Stuttgart+ANE, it's Stuttgart-WHG+ANE. The North Caucasus and Druze model essentially Stuttgart-WHG+ANE in Laz formal models, and Armenians fit a point on a cline between North Caucasus and the Levant.

ryukendo kendow said...

What Razib's been saying seems quite clear IMO.

Razib points out that Laz found that eastern and western HGs are distinct, and that Yamnaya is closer to Eastern than western.

I think what's probably happening is Laz is postulating the existence of a metapop 'Eastern HGs', from which the Karelian and Sammara derive, which is as Razib said closer to Malta than to Western HG. Yamnaya differs from Karelian+Sammara by having Near Eastern + Caucasus ancestry, where the NE/Cauc portion seems to be represented best by Armenians, at approx 50%.

This is then diluted into Corded Ware at 70% contribution, to produce a 0.5X0.7~36% 'Karelian', aka Eastern HG contribution into what used to be a relatively pure WHG area.

The variable here is how far towards Mal'ta the Karelians were. The fact that Karelians and Yamnaya were mentioned in the same breath prob means ancient DNA was involved here.

Chad Rohlfsen said...

Well, let's try this then...

Armenian is 86% NE, 14%ANE

Karelian is 70% WHG, 30% ANE

43%NE, 35%WHG, 22% ANE

The EEF model might look more like 58% EEF/ 20% WHG / 22% ANE. If this is 75% of Corded Ware, then the natives of Poland and the Baltic, may have only been 15%EEF, 75% WHG, 10% ANE, at the end of the Neolithic.

Even at just 50% EEF, Poland and Norway could only be at the most 20% EEF, post-Neolithic, to allow for the reduction to 42% EEF.

True revenge of the hunter gatherers in Europe.

Chad Rohlfsen said...

David,
If Armenians were only 10, and Karelians 20, that would be 15% ANE, its 50/50 of each.

Davidski said...

Ah, OK. Well let's hope Razib blogs about this to clear up a few things.

Davidski said...

Hang on, here's that paper with those Karelian samples IMO.

http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003296

Davidski said...

OK, so the ancient Karelians from near the White Sea had:

2x U2e

2x U4

U5a

H

3x C1

They could well have been mostly ANE based on that, if they also carried Y-HG Q and/or R.

Chad Rohlfsen said...

David,
Did you see the Bell Beaker site in NE Poland, near the Belarus border?

ryukendo kendow said...

@ Chad
If the Karelians were mostly WHG, Razib would have said it IMO.
Here's what he actually said:
Eastern HG away from western HG, Yamnaya toward one, Mal'ta
Eastern HG from Karelia and Sammara. ANE related to Eastern HG. Yamnaya had near East and Caucasus.
ANE in Europe from eastern HG groups? (via yamnaya)
The picture seems clear.

Chad Rohlfsen said...

German Beaker
U2e
W5a
I1a1
K1
U5a1
T1a

Looks like it could be the same 50/50 mix.

Chad Rohlfsen said...

Karelians cant be mostly ANE, That would make Yamnaya over 32% ANE. Considering that all of us in Northern Europe are mostly Yamnaya, it puts ANE too high for modern pops.

Chad Rohlfsen said...

Yamnaya being so Near East/EEF, means that the Mesolithic survival in Northern Europe, is huge. There will be ANE there already. They cant be inputting more than 15%. 20-25% ANE seems about right.

Average Joe said...

Anglo-Saxon input is minimal, apparently.

Not necessarily. It is likely that most of the Anglo-Saxon invaders were male and so would have mated with the native British females. Any genocidal activities would have concentrated on the native British males.

Chad Rohlfsen said...

Average joe,
Any kind of genocide would yield us graves. Remains are too hard to find, to suggest that.

Chad Rohlfsen said...

The authors are clear that modern Brits are more like the Iron Age samples.

Chad Rohlfsen said...

R1a1a & R1b coalescent 5k BP each. Both coalesce with each other 10k BP. 30x coverage

Same source, same migration?

Nirjhar007 said...

Please someone tell me there is some data in hand now on Y-DNA of Samara!

Nirjhar007 said...

''Yamnaya had near East and Caucasus.
ANE in Europe from eastern HG groups? (via yamnaya)
The picture seems clear.''
Superb!

Chad Rohlfsen said...

David,
For your proto-IE, how about something like St11+Georgians, to make up that extra ANE, to get to 25%ANE. Or if you want to stick with Armenians, throw some AG2 into a Motala hunter. Whatever it takes to get to 25%ANE. It would be interesting to see a k4, for Europeans. Use that proto-IE, Loschbour+LaBrana, Stuttgart+Otzi, and then some Motala Hunters. Just to see if it shows Northern Europeans as 2/3 Yamnaya.

Davidski said...

Corded Ware were 75% Yamnaya, not modern Northern Euros. We're all probably less Yamnaya than that. I suspect the reason the Corded Ware samples clustered in North Central Europe was because they were projected onto a PCA plot.

barakobama said...

Modern day inhabitants of Russia are probably more similar to Yamna than previously thought.

Since it seems Yamna may have contributed as much as 50% ancestry or more to NE and NW Euro, it must be one way or another why they both basically have the same pigmentation trend(Also they have many of the same pre-IE ancestors), which didn't exist in the stone age. The Mesolithic HG type obviously doesn't exist to a large extent anymore, the Neolithic-descended type is very similar to modern middle easterns(Sardinians are great evidence), the bronze age add on which had mixed ancestry from Mesolithic and near eastern-types, is the N European-type.

Even though Yamna was darker than modern west Asians(mostly because of eastern hg, ANE), things obviously changed later on. Yamna-descended Andronovo in central Asia had the pigmentation of N Europeans, so Yamna must be one way or another why it exists in Europe and did not in pre-IE times. Most of our physical appearance is probably from post-Neolithic selection(it could have been created by the human mind in some ways, and didn't have an obvious survival advantage) and is therefore very differnt from our stone age ancestors.

Chad Rohlfsen said...

Here's a paper with radiocarbon dates for Poland: https://www.academia.edu/2022469/Nor...kers_in_Poland

Southern Poland: The sum of probability distribution of all the calibrated dates stays in the interval between 2470 and 2270 BC.
The agglomerations are closely related to their Czech and Moravian counterparts.

Iwno Culture: The sum of probability distribution of all the calibrated dates obtained for the Iwno Culture stays between 2210 and 1880 BC.
In the Polish Lowlands the Iwno Culture emerged, a syncretic unit that combines traits of Bell Beakers, the Single Grave Culture and, to a lesser degree, early Únìtice Culture.

Chad Rohlfsen said...

Corded Ware couldn't be much more ANE than modern inhabitants of the area. Corded Ware has no expansions out of its area to explain the near level ANE across all of Northern Europe. I suspect that Bell Beaker will be very similar. Check out that link for another Beaker site, alongside Corded Ware.

Chad Rohlfsen said...

https://www.academia.edu/2022469/Northern_and_Southern_Bell_Beakers_in_Poland

Bell Beaker movements appear to mimic that steppe group from the Black Sea. Remember the Kromsdorf Beakers were shown to come from a good distance to the NE. Which would probably be Poland, or there about.

Chad Rohlfsen said...

Polish Beaker graves even had earrings of the same type that appear in Ireland, later.

barakobama said...

Chad,

"David,
For your proto-IE, how about something like St11+Georgians, to make up that extra ANE, to get to 25%ANE. "

He shouldn't do that because Laz generally said Yamna was 50% Karelian hg and 50% Armenian. We can only guess exactly what their EEF-WHG-ANE was. I guess he could do a speculative test, like the mammoth steppe one though.

"Corded Ware has no expansions out of its area to explain the near level ANE across all of Northern Europe. I suspect that Bell Beaker will be very similar."

Bell Beaker-Corded Ware-Unetice in central Europe were very similar, there's ancient mtDNA prove of that. It's probably safe to say Indo Europeans brought ANE(at least most) to west Europe. Why R1a-M417 is so rare, why west and east are split in admixtures, how it got there without Corded ware, etc. is up to debate. I was hoping they'd tell if R1b-L23 suddenly popped up in the copper age or did not, so we know if it's likely an Indo European lineage or not.

Chad Rohlfsen said...

R1a1a & R1b coalescent 5k BP each. Both coalesce with each other 10k BP. 30x coverage

This was all Razib had on the subject. I'm trying to ask him now.

ryukendo kendow said...

@ Davidski
Agree.

@Barak
"Modern day inhabitants of Russia are probably more similar to Yamna than previously thought. "

This is literally disproved by the tweets.

@ Chad
Why is mtHap H so common among Beaker remains, and where do you think it comes from?

Matt said...

Chad: Well, let's try this then...
Armenian is 86% NE, 14%ANE
Karelian is 70% WHG, 30% ANE
43%NE, 35%WHG, 22% ANE
The EEF model might look more like 58% EEF/ 20% WHG / 22% ANE. If this is 75% of Corded Ware, then the natives of Poland and the Baltic, may have only been 15%EEF, 75% WHG, 10% ANE, at the end of the Neolithic.


Chad, nice check, I think these numbers are basically going to be on the money, although there's still the possibility ANE could be higher in "Karelian HG" (if that is truly what we have) given that existing papers seem to show it may increase from Motala to the Gotland PWC hunter gatherers, unless that's an artefact from different methodologies. We'll have to wait if Razib meant "EHG are more like ANE than WHG are, but still closer to WHG by far" or "EHG are more like ANE than they are like WHG".

Although it surprised me that they have such high Near East, but that's the case if they truly model as 50% Armenian (and not as actually 40%-45%) regardless of what the HG portion is like.

This does mean that Europe would not really, based on these tweets, fit really a Stuttgart->Yamnaya cline, as many Northern Europeans are less Near East like than a Yamnaya->Stuttgart mix would be.

I think you've suggested this might be from extra survival by local HG groups all across Europe getting picked up, which is possible (given local tract sharing, etc). Correct me if I'm getting you wrong on this.

But I wonder if it might not also be instead (and more simply) Corded Ware may have just had an extra 25% WHG+ANE (in some blend) compared to Yamanya, as after all Razib only described Corded as 75% Yamnaya, without specifying their other portion. It's the simplest possible idea that Corded were Yamnaya + LBK, given they moved into LBK territory, but...

If Yamnaya is 43%NE, 35%WHG, 22% ANE, and Karelian is 70% WHG, 30% ANE, as in your figures, and Corded is 75% Yamnaya and 25% Karelian on top, then Corded would be 32.25% NE, 43% WHG, 24% ANE. Which *would* fit a far point on a European cline...

I'd be interested to see where a Scandinavian hunter gatherer+South Caucasian merge would be as well, whether or not we agree that's how it happened.

Davidski said...

I've just been told that Corded Ware had a lot of ANE, whatever that means, while Bell Beakers had much less.

Anyway, let's take this here...

http://eurogenes.blogspot.com.au/2014/10/pie-homeland-update-paleogenomics.html

I might be able to get some more details soon.

Grey said...

@Chad

"No Saxon replacement.. modern Brits are more like the Iron Age samples."

Or

Saxon replacement of a Belgae upper layer (originally from roughly the same region) followed by gradual mixture with a mtdna substrate

identical to an earlier Belgae replacement of a previous upper layer followed by their gradual mixture with the same surviving mtdna substrate

identical to an earlier unknown replacement of a previous elite followed by their gradual mixture with the same surviving mtdna substrate

etc

repeated however many times there was a coastal invasion from roughly the same regions over the centuries.

This would lead to a recurring pattern of periods where there is an unmixed upper layer (e.g. Hinxton) interspersed with periods where the previously upper northern layer and earlier substrate layer have become a single mixed population.

Grey said...

@average joe

"Any genocidal activities"

You don't need that. All you need is two population layers with different status.

If you have a conquest leading to an upper population layer (say 40%) over a lower population layer (say 60%) then over time you will get mostly male mediated gene flow from the upper layer to the lower layer.

Eventually you get a population that is mixed autosomally but with the y dna almost exclusively from the original upper layer.

Even more so if that process had been repeated multiple times by different invaders with the same y dna.

Grey said...

@chad

"If these Bronze Agers are 40-50% farmer, then that means we may have only had a 50% replacement during the Neolithic, for Northern Europe."

Or there was an up to 90% farmer replacement (less than 90% in mtdna) followed later by a reverse and an up to 90% backflow (less than 90% in mtdna) followed by admixture of the varying proportions.

Graham Little said...

I read that over on one of the dna forums. That one and four are the Iron age Britons. Reason being is that all the Anglo Saxons were women.

Which now makes sense on the Y-Dna and Felix's time estimate.

Simon_W said...

Is there any credible source for the claim that all Anglo-Saxon samples are female? To me that's hard to believe given that in the K15 Oracle Hinxton 1 - 3 are all closest to Orcadians, whereas Hinxton 4 is closest to the Irish. Moreover in the mixed population results, Hinxton 1 is closest to 75% Orcadian + 25% West_Norwegian. That doesn't sound like a native Celt of Britain, more like someone with Germanic links.

Davidski said...

Yes it's confirmed that the two males are from the Iron Age and the three females from the Anglo-Saxon period.

There's certainly a difference between Hinxton1 and the two females. It's not as pronounced as between Hinxton4 and the two females, but clearly Hinxton1 is less eastern than them.

The fact that Hinxtons 1, 2 and 3 are best fitted as Orcadians in the oracles could mean a lot of things, but I think the main thing it means is that they're all genomes from near the North Sea.

I'll do a Hinxton ancient genomes roundup next week after I publish Hinxton5's results.

ZeGrammarNazi said...

Who confirmed Hinxton's 1 and 4 are the Iron Age samples, David?

Using the least squares method and the Eurogenes K15 run we get this for Hinxton #5:

#1 13.28
#2 13.72
#3 18.04
#4 7.06

Also, while 4 and 5 have more Baltic than the other three, 1, 2 and 3 have more Eastern Euro and West Asian than 4 and 5.

My initial thought was that 1, 2 and 3 are more Corded Ware-influenced due to their elevated Eastern Euro and West Asian scores and likelt from the from the AS period, and the Baltic component might represent WHG-like ancestry shared between the Iron Age Brits and the Baltic region.

However, if has been confirmed by the authors that 1 and 4 are the Brits, then the K13 results are much more accurate than the K15.

ZeGrammarNazi said...

Correction: The West Asian scores between Hinxton's 1, 2, 3 and 4 are comparable. Hinxton 5 has 0%.

The Eastern European correlation between the samples that I mentioned earlier still stands, however.

Davidski said...

It was confirmed at the ASHG talk. We also have it in print here.

https://www.sciencenews.org/article/anglo-saxons-left-language-maybe-not-genes-modern-britons

ZeGrammarNazi said...

Thank you.

Here are the results when you use the least-squares method and the K13 data to compare H-4 to the other samples:

#1 3.91
#2 6.01
#3 7.17
#5 9.62

That is more accurate to the data than the K15 results.

Fanty said...

"anglo-saxons-left-language-maybe-not-genes-modern-britons"

Hmm.

I always thought this:
http://cache.eupedia.com/images/content/Haplogroup-R1b-L21.gif

To be the Y-DNA of the Iron Age Brits

and this:

http://cache.eupedia.com/images/content/Haplogroup-R1b-S21.gif

To be a marker left there by varius Germanic input like Anglo-Saxons or Vikings.

Wich apears... whats it? 20-30% this marker alone.

So, if modern Brits have almost no Germanic autosomal DNA... does this mean....

a) this Y-DNA marker is not "Germanic" at all but a lot of them Celts had it aswell

or

b) You can easily get an Y-DNA marker to hit 30% while the autosomal DNA is almost non-existent?

Grey said...

@Simon_W

"That doesn't sound like a native Celt of Britain, more like someone with Germanic links."

I think prior thinking is distorting people's view.

There's been an idea for a long time that "Celtic" and "Germanic" were distinct both culturally and physically but in the remoter corners of the UK and Ireland you can still physically see that's not true.

I think there were clearly three distinct groups:

1) southern genetics with Celtic culture
2) northern genetics with Celtic culture
3) northern genetics with Germanic culture

with
(1) still around in parts of North Wales (and corners of Ireland)
(2) still around in parts of Scotland and Ireland
(3) still around on the east coast of England but mostly merged with (1) in the rest of England and South Wales

Simon_W said...

Well, if the Iron Age Brits were partly Orcadian-like and partly Irish-like (perhaps 1 and 4 were from different tribes? Iceni and Catuvellauni, e.g.), and the Anglo-Saxons Orcadian-like, then they were on the whole quite similar to each other.

On the topic of y-DNA vs autosomal admixture: R1a1 on the Orkneys is 34.2%, and most of it must be from Norwegian Vikings. Who probably weren't 100% R1a1, so according to y-DNA the Norwegian impact was considerable, but autosomally the Orcadians are much closer to the Western Scottish than to present-day Norwegians.
And then there's also the example of the Basques who are 80% or more R1b, and yet one of the most Mediterranean and least ANE admixed populations of Europe.

Simon_W said...

The Anglo-Saxons seem a bit more eastern and more continental partly, but no matter if Irish, Scottish, Orcadian or Anglo-Saxon, you can throw them all into a northwest European category that differs from the modern-day north European and central European categories.

Grey said...

@Simon_W

"The Anglo-Saxons seem a bit more eastern"

Yes, I think the basic mechanic is a 400 year, or 600 year or 800 year sea raider -> settled farmer cycle (like a maritime version of the steppe raider -> farmer cycle) coming from the same north sea source region but with each wave having more eastern euro mixture than the previous wave.

(more blond, less red?)