Part 2: 8,000 years of Natural Selection in Europe.

Still no basal R1a and R1b there? ;)

Nice to have new results.
 
Y-DNA J in an EHG individual from Karelia 5500 BC. J2a1 in Barcin in 6500-6200 BC. No R1b in the Chalcolithic samples from Atapuerca.

What was that? the 25% of Teal in EHG and 50% in Yamna came all from female teal wives taken captive by "horny" EHG groups?
This will be hard swallow for all the supporters of the "Teal wive" theory. :D

So much to that. I go so far and say a good chunk(Not all) of the R1b in EHG and the l23 in Yamna was also coming together with J.
 
I was always proposing a "Teal " ancestry for J Haplogroups. (EEF + ANE). The J in Barcin can be from contacts to Eastern farmers (as per paper J was rather a minority lineage in Anatolian farmers) and the J in EHG samples is just a prove that they were already in contact with Teal farmers and therefore even SOME branches of the R1b in those EHG groups might have come together with J and be founder effect.

At least it proves that the wive theory is complete bogus.
 
What was that? the 25% of Teal in EHG and 50% in Yamna came all from female teal wives taken captive by "horny" EHG groups?
This will be hard swallow for all the supporters of the "Teal wive" theory. :D

So much to that. I go so far and say a good chunk(Not all) of the R1b in EHG and the l23 in Yamna was also coming together with J.

You don't understand. The J EHG guy came from the same site a R1a1* guy was form, that R1a1* had no Near Eastern ancestry. The J is probably a less succesful brother of I that came to Europe 10,000s of years ago. The three new Eneolithic Samara guys all had EHG Y DNA and 1/3 had Near Eastern mtDNA. It supports the Teal wives theory.
 
You don't understand. The J EHG guy came from the same site a R1a1* guy was form, that R1a1* had no Near Eastern ancestry. The J is probably a less succesful brother of I that came to Europe 10,000s of years ago. The three new Eneolithic Samara guys all had EHG Y DNA and 1/3 had Near Eastern mtDNA. It supports the Teal wives theory.
So now J is not a farmer/herder Haplogroup anymore because it destroys the mighty H&G stole wives theory?
Unlikely, J is found in Neolithic context from Eastern farmers all the way to Western farmers. If J made it to EHG with "no sign of southern admixture" , so why shouldn't we assume the same for some R1b in EHG? What if South_Central Asian and Iranian Plateau samples turn out Teal and even EHG like?

So many possibilities. still open.
 
Revised Mathieson et al paper on 8,000 years of selection in Europe

OOPS! :)
I've been working on a thread about this since I got the feed, but you guys beat me to it, so I just moved my post over here.

Well, Lazaridis mentioned that the revised Mathieson paper that would contain a lot of information from his paper as well as a lot of new samples would appear in a revised preprint, and it has:

Here it is:
8000 Years of Natural Selection in Europe revised
http://www.biorxiv.org/content/biorxiv/early/2015/10/10/016477.full.pdf

I've skimmed it, but there's a lot in here, so I can't summarize much of it at this late hour.

My major takeaways that weren't already sort of telegraphed:

Anatolian farmers already carried SLC24A5, apparently, so increased frequency in Europe is because of migration.

They were 47% G2a. We'll have to wait for the Lazaridis paper for more info apparently.

They don't think it necessarily means that the migration to Europe started from Anatolia. They also don't know precisely how wide the spread was in the Near East of this particular group. However, whether the migration went by sea (Cardial) or by land (presumably into and out of the Balkans), it all came from this type of farmer.

The EEF picked up 7-11% WHG initially.

The El Mirador Cave Chalcolithic people from Spain are genetically similar to the MN Iberians and thus have more WHG than their EN predecessors, but their WHG is about the same as that of the MN Spanish (23-28%), and they have no steppe ancestry, where as people in Central Europe from this time period did have some.

The mixture of EHG and an Armenian like group began about 5200 BC, "with some individuals resembling EHG and some resembling Yamnaya". The proportion was about 74%/26%.

Yamnaya from Samara, the Afansievo people (3300-3000BC), and the Poltavka people later on (2900-2200 BC) that followed Yamnaya on the steppe are all homogeneous and are predominantly R1b (one Poltavka sample is R1a), and their Armenian like Near Eastern ancestry ranges from 48-58%, but without Anatolian like ancestry.

After Poltavka, Srubnaya became 17% Anatolian Neolithic or EEF, perhaps because mixed steppe/farmer groups from the west moved east.

Previous work (Allentoft presumably) suggested this type of ancestry went east to Sintashta by means of a Corded Ware migration.

However, according to this Lab, the fact that Srubnaya also harbored such ancestry indicates this Anatolian Neolithic or EEF ancestry could have come from a more eastern source. Further evidence that it was not Corded Ware is the fact that Srubnaya exclusively carries 4 R1a Z93 (as did one Poltavka sample).

Also very interesting is the fact that in Khvalynsk III there was R1a, R1b, and Q1a. Also, there is that one R1a in Poltavka. Therefore, the seeming shift from R1b to R1a on the steppe does not necessarily mean that new populations migrated onto the steppe. R1a might have been in Samara but not included in the rich burials associated with Yamnaya and Poltavka.

(Goodness, what a disappointment for those who were positively panting for a R1a/R1b war. :))

Also very interesting is that outside the steppe they found an individual from Karelia who was autosomally EHG but was yDna J. That was 5500 BC, not too far from the 5200 BC and start of Armenian like appearance.

I'll leave the selection stuff until tomorrow.

Oh, and J2a1 in Barcin Neolithic.
 
163 samples, sweet. We should be getting some statistical certainty. I'm a bit disappointed though, there is not even one sample from Cucuteni, Maykop or Natufian/fertile crescent.
 
So now J is not a farmer/herder Haplogroup anymore because it destroys the mighty H&G stole wives theory?
Unlikely, J is found in Neolithic context from Eastern farmers all the way to Western farmers. If J made it to EHG with "no sign of southern admixture" , so why shouldn't we assume the same for some R1b in EHG? What if South_Central Asian and Iranian Plateau samples turn out Teal and even EHG like?

So many possibilities. still open.

Alan, I'm not sometype of raciest. I don't think EHG were inherently super masculine and superior to Near Eastern males. Why would I anyways, I have very little EHG in me. Stop taken this stuff to a personal level. The J in Mesolithic Karelia could very well be a brother to hg I that WHGs carried. EHG had mtDNA U5a and WHG U5b, J and I split around the same time. J in Mesolithic Karelia isn't good evidence their *dead* forms of R1a and R1b came from the Near East.
 
Also very interesting is that outside the steppe they found an individual from Karelia who was autosomally EHG but was yDna J. That was 5500 BC, not too far from the 5200 BC and start of Armenian like appearance.

I'll leave the selection stuff until tomorrow.

Oh, and J2a1 in Barcin Neolithic.
Personally I believe that R1a has lesser to do with PIE than J2a and even R1b. R1b is also not a real 'archaic' PIE marker, but it is the marker the spread heavily into Europe from Yamnaya and caused a founder effect.

But folks who Indo-Europized Yamnaya were most likely J2a and some R1b from the Iranian Plateau (/Leyla Tepe).
 
Some useful links. I posted a few earlier.

List of Mathieson samples.

Extended Data Mathieson useful information
Updated Ancient West Eurasian Y DNA.
Updated Ancient West Eurasian mtDNA.

Selection
SNPs under strongest selection have to do with: Lactase persistence(rs4988235) and Skin Color(rs16891982). Next for highest selection Immunity(?, rs2269424 and rs4833103).
>First Europeans with derived alleles in rs4988235 is LN/BA Central Europeans and closely related Central Asians but at very low 8%. Today a similarly low frequency exists in Tuscany, but a high frequency exists in Spain and very high frequency in NW Europe(CEU, GBR).

>Mesolithic Swedes and Neolithic Anatolians had a decently high frequency of derived alleles in rs16891982, with 40% in Anatolia(maybe 1/5 having 2 derived alleles). Slightly lower frequencies existed in Neolithic Europe. Frequency rose with LN/BA Central Europeans and their close relatives in Central Asia at 70%+. Today there's an almost 100% frequency in NW Europe and Tuscany, and 80% frequency in Spain.

>Mesolithic West and Swedish Europeans were 100% Blue eyed(with the data we have, N=11). Neolithic Anatolians were about 80-90% Brown eyed. A similar high frequency of Brown eyes existed in Yamnaya, Afanasievo, and Potapovka. Brown eyes slightly rose in frequency in Central Europe with Steppe-admixture. Tuscans and Spanish have similar eye-color frequencies as Neolithic ones but NorthWest Europeans have a higher frequency of Blue eyes than their Late Neolithic ancestors.

>Derived allele in rs4833103 was non-existent in West and Swedis hunter gatherers. It was at a low frequency in all other ancient Europeans, of 5-15%. Today it is at 55%+ in NorthWest Europe and 40% in Spain and Tuscany.
 
Alan, I'm not sometype of raciest. I don't think EHG were inherently super masculine and superior to Near Eastern males. Why would I anyways, I have very little EHG in me. Stop taken this stuff to a personal level. The J in Mesolithic Karelia could very well be a brother to hg I that WHGs carried. EHG had mtDNA U5a and WHG U5b, J and I split around the same time. J in Mesolithic Karelia isn't good evidence their *dead* forms of R1a and R1b came from the Near East.

Look, who actually defended the ydna J is not EEF but a EEF+Teal merging idea based on the fact that it is close cousin of I? ME

BUT the point is that J is Obviously connected to farming /Herding cultures why is it so hard to understand. All other J samples are in Teal and EEF context. But than we have one Keralian J who has no autosomal sign of anything farmer like. That brings us back to our (Angela and me) initial theory, that this and as well some of the R1b in Samara H&G could be founder effect and through mixing with local WHG groups the Teal could have been so deluded until it autosomally disappeared.

So if there is J without any sign of farming genes in Karelian, there is R1b in Neolithic Iberian without any sign of EHG admixture. Why shouldn't it be possible that the autosomal DNA got deluted in both groups?
 
Arame wrote this

Kurti

Congrats! Your theory about missing clusters on the PCA seems to be correct. The IA Scythian is on a "empty" place on modern populations PCA. Well it is right on the place where other Bronze Age Steppe samples are. It seems the Turkish invasions and later the Slavic expansion had a dramatic impact on the Steppe populations.


Anyone remember my theory? I was laughed at for it. They call me insane until my theories are confirmed it's always the same :)

http://www.eupedia.com/forum/threads/30706-Europe-West-and-South_Central-Asia-and-the-unnatural-gap
 
Look, who actually defended the ydna J is not EEF but a EEF+Teal merging idea based on the fact that it is close cousin of I? ME

BUT the point is that J is Obviously connected to farming /Herding cultures why is it so hard to understand. All other J samples are in Teal and EEF context. But than we have one Keralian J who has no autosomal sign of anything farmer like. That brings us back to our (Angela and me) initial theory, that this and as well some of the R1b in Samara H&G could be founder effect and through mixing with local WHG groups the Teal could have been so deluded until it autosomally disappeared.

So if there is J without any sign of farming genes in Karelian, there is R1b in Neolithic Iberian without any sign of EHG admixture. Why shouldn't it be possible that the autosomal DNA got deluted in both groups?

Good point. Yes the autosomal DNA of the R1b1 and J ancestor of Neolithic Anatolia and Mesolithic Russia was diluted. However the majority of EHG probably had R1b and R1a. The chances of two separate Near Eastern lineages becoming both popular and leaving no autosomal in-print is low. Maybe a non-Basal Eurasian influenced people in West Asia are the source. But Teal almost certainly is not. Teal could be the source R1a-M417 and R1b-M269 but not of EHG's basal forms of R1b and R1a.
 
Some other interesting things in the paper. One I already alluded to...no E-V13. There's also no R1b V88.

Now, this is only one area, and yet they had a large mix of yDna, even if G2a predominated, so, it's possible we'd find both in another group in Anatolia or further south, yes?

Those groups would have had to be the same autosomally though, given that the authors say that both Cardial migrations and LBK type migrations stemmed from one rather homogeneous group?

Speaking of the Ydna in Anatolia: Anatolia_Neolithic: Y haplogroup:
G2a: 7
G: 1
H2: 2
H: 1
I: 1
I2c: 1
C1a2: 1
J2a:1

So, the I and C lineages aren't a very big part of the whole. I wonder if someone will try to get a better fix on the I and the J2a.

Ed. There was one H2 and one H.
 
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Yes, I noticed the high amount of farmer. That certainly wasn't the impression I was getting from the internet chatter over the last months.

It would have been interesting had they done that kind of analysis for modern people.

Hobby groups will always explain you the facts in their own preffered way.

Sintashta EEF seems 15% more than among Corded Ware. Which brings the schoolers of the paper to the conclusion that we aren't dealing here with an Eastward migration of Corded Ware groups, but a group which is ancestral to Corded Ware as well Sintashta. And it seems like Andronovo indeed was absorbing Yamna (Teal and EHG ) like ancestry in Central Asia which brings me to the conclusion that something Yamna like was living there.
 
Yes, I noticed the high amount of farmer. That certainly wasn't the impression I was getting from the internet chatter over the last months.

It would have been interesting had they done that kind of analysis for modern people.

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there is a shift toward neolithic but still in the neigbourhood of Yamnaya/Afanasievo/Poltavka
notice Bell Beaker/European BA have the same shift, even a little bit more pronounced
 
Some other interesting things in the paper. One I already alluded to...no E-V13. There's also no R1b V88.

Now, this is only one area, and yet they had a large mix of yDna, even if G2a predominated, so, it's possible we'd find both in another group in Anatolia or further south, yes?

Those groups would have had to be the same autosomally though, given that the authors say that both Cardial migrations and LBK type migrations stemmed from one rather homogeneous group?

Speaking of the Ydna in Anatolia: Anatolia_Neolithic: Y haplogroup: 7 G2a, 1 G, 2 H2, 1 H, 1 I, 1 I2c, 1 J2a, 1 C1a2
G2a: 7
G: 1
H2: 2
H1: 1
I: 1
I2c: 1
C1a2: 1
J2a:1

So, the I and C lineages aren't a very big part of the whole. I wonder if someone will try to get a better fix on the I and the J2a.

this is only a very small part of Anatolia, from 2 sites nearby in NW Anatolia

R1b I would expect further east, maybe south of Caucasus , so no R1b-V88 here
E-V13, I'm getting more and more convinced the proposed TMRCA time of 4300 years is +/- correct
biggest surprise to me was to find I2c, which uptill now hasn't been found in the neolithic
all others were in early European neolithic
except H1, but I don't find it in the list (I have H) ; is it a typo or did you find some suplementary info?
 

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