36,200YBP European genome

[Greying Wanderer]

Neolithic farmer long before Neolithic farming in Russia. Interesting. Is this Neolithic farmer about same thing as EEF?

I think that's the idea. If it's right I think it's saying basal isn't a clear signal of neolithic i.e. the first farmers came from a pop. that had a lot of it but some of the WHG or ANE pops. may have some as well. I may be misunderstanding.

 

[Maciamo]

I still don't understand how it is possible to map the available autosomal DNA from such old samples to contemporary human populations always by 100%. Shouldn't there be always a piece of unmappable DNA, and the older the sample the more unmappable DNA? Even if that ancient individual successfully created long-lasting and flourishing offspring to this day, there was still drift, and drift means loss by replacing older nucleotides by newer nucleotides, either due to mutations or crossover. Or am I wrong? I feel this is probably a naive question, but somehow I don't see or remember the answer at this moment.
If I'm right about unmappable DNA, then this could already explain the neolithic share in the Kostenki sample.

Exactly. That's why I propose to see what percentage of those ancient genomes survive in modern populations. Trying to paint modern admixtures on Palaeolithic genomes will always get lots of noise or nonsensical data. It's a bit like looking at a modern European genome and trying to paint admixtures using only East Asian populations as comparison. You might get a overall picture that looks 20% Japanese, 15% Korean, 25% Mongolian, 20% Han, 10% Miao-Miao and 10% Vietnamese, even if that European sample actually has 0% of any of these admixtures.

 

[bicicleur 2]

Exactly. That's why I propose to see what percentage of those ancient genomes survive in modern populations. Trying to paint modern admixtures on Palaeolithic genomes will always get lots of noise or nonsensical data. It's a bit like looking at a modern European genome and trying to paint admixtures using only East Asian populations as comparison. You might get a overall picture that looks 20% Japanese, 15% Korean, 25% Mongolian, 20% Han, 10% Miao-Miao and 10% Vietnamese, even if that European sample actually has 0% of any of these admixtures.

probably more than half of Europeans descend from R1b-L11 or I1 or R1a-Z282 and TRMC of the eldest these 3 is probably no more than 6000 years
EEF-WHG-ANE was invented to compare todays populations with genomes of some 8000 years old skeletons of which I allready doubt relevance
we're waisting our time trying to explain our relations with skeletons 20000 years old or older
most single skeletons 20000 years old or even 8000 years old are extinct lines, so they are only linked with todays populations through their ancestors who are several 1000's years older again

 

[bicicleur 2]

i find this article about this old K-14 DNA very interesting, but don't talk about EEF-WHG-ANE in this case

 

[Greying Wanderer]

i find this article about this old K-14 DNA very interesting, but don't talk about EEF-WHG-ANE in this case

It matters though because up till now "basal" has been tied to EEF in the EEF-WHG-ANE trio so if that's not correct then it will have to be looked at again.

 

[MOESAN]

The skull looks like Cro-Magnon

I totally agree - very close to what we know - no confusion with the shapes of Combe-Capelle, Brünn or Laugerie-Chancelade - less "brutal" than Capelle/Brünn -
autosomals seem telling us they are of a same remote phylum but they developped great differences as time passed -
according to scholars, the cromanoid forms reached southeastern Europe long before the brünnoid forms (30000 BC against 9000 BC?)- I have no sound opinion concerning the places they developped their pecularities - the brünnoid forms seem more "primitive" as a whole concerning face and skull but...

 

[MOESAN]

Instead of comparing Palaeolithic genomes with modern admixtures, I think it would make more sense to look at the percentage of Palaeolithic still found in modern populations. In other words we should look at Palaeolithic genomes the other way round. What's the point of attributing modern labels to a hunter-gatherer who lived 37,000 years ago ? What's interesting is to try to find out what percentage of that ancient genome left contributions in the modern gene pool, just like for Neanderthal.

By the way, the paper says that they identified (only) 0.9 ± 0.4% Neanderthal ancestry in K14, as opposed to 2.4% ± 0.4% in La Braña, and about 2% in modern Eurasians. They estimate the age of the Neandertal admixture at approx. 54,000 years ago (so most likely in the Middle East since Cro-Magnons had not yet reached Europe back then).

all that is a set of approximative tools I think - but I find it 's interesting doing the two ways, in fine they tell us close things about the links between ancient and current populations being the only difference the fact common genes are more evidently passed from ancient to modern (and sometime, passed to both by an even more ancient population -

 

[Fire Haired14]

Lots of noise when compared to modern populations, as expected from such an old sample.

The three main matches are: Mesolithic European, Middle Eastern (Neolithic farmer) and South Asian. That corresponds to the wider definition of the Caucasian racial group.

F3, f4, and D-statics show K 14 follows the same pattern as Mesolithic western Europeans(30,000 years later!!!) in terms of relation to modern people. He's also closer to MA-1 than to any modern pops, and even closer to Mesolithic western Europeans, but closer to Loschbour than to La brana-1 and Motala12. Even if K 14 had some of whatever "basal Eurasian" is, he was still mostly from the same source as Mesolithic western Europeans and MA-1.

http://geogenetics.ku.dk/latest-news/k-14

You should watch the video in that article. This is pretty incredible news. All the components of ancestry that make up modern Europeans(and the vast majority of west Asian's ancestry) existed in K 14 who lived ~37,000 years ago. K 14 reveals that at least ~37,000YBP Mainstream-Eurasian split into a "western" group who diversified(WHG,ANE) and gradually mixed with each over a course of some 30,000 years and in an area spanning from Portugal-Siberia. They mixed with east Asians during the UP, to create native Americans, and must have had a strong presences further south in west Asia, south Asia, and north Africa. Europeans are simply a mix of "West Eurasians" who had been living north of the Caucasus pretty much uninterrupted for 10,000's and years and west Asians who were a mix of their relatives and "Basal Eurasians".

Another interesting factoed learned through this study(and also those 2 from late year) is that Native Americans are more "west Eurasian" than many middle easterns.

 

[bicicleur 2]

C-M130
C1-F3393
C1a-CTS11043
C1a2-V20 = the old C6 like La Brana and neolithic Hungary

which is this Kostenki?

isoggId haplogroup position mutation K14 depth isDamage

F3393 C1 23023974 C->A A 1 FALSE

what does this mean
he tested C1 but the result is not reliable?

 

[joeyc]

Interesting that he had less "North Euro" admixture than the Paleolithic Siberian Mal'ta. But this Russian had both Middle Eastern and African admixture, so probably he had Basal Eurasian.

The lack of Neanderthal ancestry is not a surprise. Neanderthal admixture in Europe came from Siberia with Mal'ta and the like.

 

[Angela]

I don't know if everyone saw the article in Science Magazine about the study. (It's rather disheartening how sloppy the reporting is even in science venues.)
http://news.sciencemag.org/archaeol...genetic-identity-may-stretch-back-36000-years

This is Willerslev's interpretation of his own data:
Willerslev says the data suggest the following scenario: After modern humans spread out of Africa about 60,000 years ago, they encountered Neandertals and interbred with them, perhaps in the Middle East. Then while one branch headed east toward Melanesia and Australia, another branch of this founder population (sometimes called “basal Eurasians”) spread north and west into Europe and central Asia. “There was a really large met-population that probably stretched all the way from the Middle East into Europe and into Eurasia,” Willerslev says. These people interbred at the edges of their separate populations, keeping the entire complex network interconnected—and so giving the ancient Kostenki man genes from three different groups. “In principle, you just have sex with your neighbor and they have it with their next neighbor—you don’t need to have these armies of people moving around to spread the genes.”

All due respect to Professor Willerslev, that seems contradicted by the other ancient Dna from Europe already analyzed.

There are also some pertinent quotes from David Reich and Krause:

Other researchers say that this new genome is important because “it is the first paper to document some degree of continuity among the first people to get to Europe and the people living there today,” says population geneticist David Reich of Harvard University, one of the authors on the triple migration model. It also is “a striking finding that the Kostenki 14 genome already has the three major European components present that we detect in modern Europeans,” says Johannes Krause of the University of Tübingen in Germany.

But even if the man from Kostenki in Russia had all these elements 36,000 years ago, that doesn’t mean that other Europeans did, Reich says. His team’s DNA data and models suggest that Europeans in the west and north did not pick up DNA from the steppes until much later. He and Krause also think that Willerslev’s study needs to be confirmed with higher resolution sequencing to rule out contamination, and to have more population genetics modeling explain the distribution of these genetic types. The bottom line, researchers agree, is that European origins are “seem to be much more complex than most people thought,” Willerslev says.


I'll say.

Ed. As for any "African" in him, it's also in Ajv58, and I haven't read anything about him being Basal Eurasian.

 

[Alan]

Interesting that he had less "North Euro" admixture than the Paleolithic Siberian Mal'ta. But this Russian had both Middle Eastern and African admixture, so probably he had Basal Eurasian.

The lack of Neanderthal ancestry is not a surprise. Neanderthal admixture in Europe came from Siberia with Mal'ta and the like.

No Middle Eastern population has that weak Neanderthal. Most Middle Easterners are between 2-3%. In the South in Arabia it goes down to 2% but this because of addtional East African gene flow. In the North it can reach levels from 2.3 to 3.5%. Neanderthals mixed first of all in the Near East. Modern Europeans and West Asian have more "basal Eurasian" ancestry than Kostenki yet also more Neanderthal. So I doubt the weak percentage of Neanderthal has to do with his "Basal Eurasian" admixture.

 

[gyms]

Interesting that he had less "North Euro" admixture than the Paleolithic Siberian Mal'ta. But this Russian had both Middle Eastern and African admixture, so probably he had Basal Eurasian.

The lack of Neanderthal ancestry is not a surprise. Neanderthal admixture in Europe came from Siberia with Mal'ta and the like.

- Kostenki 14 actually has a slightly higher percentage of Neanderthal genes than ever observed before, and the genetic fragments that the man from Kostenki inherited from a Neanderthal ancestor are larger, not yet broken by the thousands of natural recombination events that have occurred since. This allowed us to estimate the time of human-Neanderthal admixture to 54,000 years ago.

http://geogenetics.ku.dk/latest-news/k-14

 

[Greying Wanderer]

"“In principle, you just have sex with your neighbor and they have it with their next neighbor—you don’t need to have these armies of people moving around to spread the genes.”

I'm not convinced that's true if you have lots of small, mostly stationary groups. If you imagine two populations split up into lots of clans with a fixed territory then if there's 10% bride swapping between the two opposing clans at the border and also 10% with the adjacent clan of the same population away from the border then for that second clan it becomes 10% of 10%. For the next adjacent clan three steps away from the border the chance is 10% of 10% of 10%. The fourth step away is 0.1 * 0.1 * 0.1 * 0.1 etc.


If there were two populations across north Eurasia with the border at the Urals I doubt there would be many of the eastern population's genes reaching Ireland *if* those two populations were split up into lots of small groups with fixed territories who only bride-swapped with their adjacent clans.


On the other hand if you had a region with *nomadic* HGs roaming around then maybe - so I wouldn't be surprised if the mammoth hunters were a meta population.

 

[Aberdeen]

deleted - rethinking the idea

 

[Angela]

Given the look of the skull in question, does the very "Australoid" or "Veddoid" looking reconstruction of the Kostenki young man make sense, or were the original Russian scientists imposing their interpretation of the find onto the remains?

http://news.sciencemag.org/sites/default/files/sn-bust.jpg

http://1.bp.blogspot.com/-7t4meQzsnBY/TrMu5mGheDI/AAAAAAAAH7I/RXb3Mrd69yY/s1600/Kostenki.jpg

FWIW, this is supposedly Sunghir man, also a UP Russian, from 28,000-30,000 BP:
http://donsmaps.com/images8/sunghir1.jpg

I find the cultural artifacts from the site fascinating as well. The most prominent are the so called "Venus" figurines:
http://donsmaps.com/kostenkivenus.html

Their resemblance to the figurines from Germany and the Balkans is quite extraordinary.

From the description it seems they were meant to be worn as amulets around the neck or the waist perhaps. Were they a form of sympathetic magic to ensure fertility? I have to say I find it off putting that often they don't have a head, although the Romans went around wearing reproductions of men's genitals, so I guess I shouldn't be complaining.

Extraordinary really...it would be nice to get inside their psyches for a second to "see" these things as they did.

Ed. Corrected link for Sunghir man

 

[motzart]

The lack of Neanderthal ancestry is not a surprise. Neanderthal admixture in Europe came from Siberia with Mal'ta and the like.

I am editing my post here because it is incorrect. K14 has an estimated 2.4% Neanderthal Ancestry, Ust Ishim has 2.26%. What Ust Ishim had were larger (longer) sections of unbroken Neanderthal DNA implying a more recent admixture, not more total Neanderthal DNA.



K14

f4 – ratio statistics for Neandertal ancestry
f4 – ratio statistics were used as previously described by (34) to obtain estimates of
Neandertal ancestry for all individuals (Table S15-S16), using Mbuti Pygmies as an
African population without Neanderthal admixture. We estimate < 2% of Neandertal
ancestry for most individuals, as previously reported (167). However, we found slightly
elevated levels both in La Braña and K14, with an estimated 2.4 ± 0.4% in K14 (see also
Fig. 4A). We then restricted this analysis to genomic regions without evidence for
Neandertal introgressed haplotypes in modern humans, following the coordinates of
24
archaic tracts identified in (168) – labeled akey in Table S17-S18 - and (167) – labeled
reich in the Table S17-S18 - and found 0% estimated ancestry for most individuals. For
K14 we still detected 0.9 ± 0.4% Neandertal ancestry. Our interpretation is that this is the
result if the presence of longer introgressed haplotypes in K14, due to its closer temporal
proximity to the admixture event (see SOM S13).


Ust Ishim

The proportion of Neandertal admixture in the Ust’-Ishim individual is estimated to be 2.26%,
which is not significantly higher than any other present-day individual (Table S16.3).
Table S16.3. Estimates of Neandertal mixture proportion!
Proportion Std error Z-Score
Ust’-Ishim 2.26% 0.33% 6.86
French 1.62% 0.20% 7.92
Sardinian 1.82% 0.20% 8.97
Han 2.11% 0.23% 9.06
Dai 1.66% 0.22% 7.58
Mix 1.87% 0.24% 7.64
Karitiana 1.97% 0.24% 8.05

 

[epoch]

Instead of comparing Palaeolithic genomes with modern admixtures, I think it would make more sense to look at the percentage of Palaeolithic still found in modern populations. In other words we should look at Palaeolithic genomes the other way round. What's the point of attributing modern labels to a hunter-gatherer who lived 37,000 years ago ? What's interesting is to try to find out what percentage of that ancient genome left contributions in the modern gene pool, just like for Neanderthal.

By the way, the paper says that they identified (only) 0.9 ± 0.4% Neanderthal ancestry in K14, as opposed to 2.4% ± 0.4% in La Braña, and about 2% in modern Eurasians. They estimate the age of the Neandertal admixture at approx. 54,000 years ago (so most likely in the Middle East since Cro-Magnons had not yet reached Europe back then).

A Russian called Vadim has a page up with maps comparing IBD's of ancient examples to modern populations. You especially want to check the one of Mal'ta. Although it wasn't the best example according to him.

https://verenich.files.wordpress.com/2014/10/maltaibd.png

Google Translate does a good enough job on this page to roughly make out what it means:

http://verenich.wordpress.com/2014/10/27/сравнение-двух-древних-европейцев-и-о/

 

[epoch]

I find the cultural artifacts from the site fascinating as well. The most prominent are the so called "Venus" figurines:
http://donsmaps.com/kostenkivenus.html

Their resemblance to the figurines from Germany and the Balkans is quite extraordinary.

From the description it seems they were meant to be worn as amulets around the neck or the waist perhaps. Were they a form of sympathetic magic to ensure fertility? I have to say I find it off putting that often they don't have a head, although the Romans went around wearing reproductions of men's genitals, so I guess I shouldn't be complaining.

Extraordinary really...it would be nice to get inside their psyches for a second to "see" these things as they did.

They do resemble the European venus figures. Mal'ta had different figurines added to these. Some appear dressed and others are thin stick puppets.

http://donsmaps.com/images24/maltafigurineshermitage.jpg
http://donsmaps.com/malta.html

Don compared these stick puppets to Eskimo children toys. However, I found that the Siberian Ket people actually had similar dolls they dressed up and all that were considered "household deities". The Ket are partly decendant of Mal'ta boys population, as that IBD map shows:

https://verenich.files.wordpress.com/2014/10/maltaibd.png

http://upload.wikimedia.org/wikipedia/en/1/10/Dolls_of_the_Ket_people.jpg
http://en.wikipedia.org/wiki/Ket_people

Of great importance to Kets are dolls, described as "an animal shoulder bone wrapped in a scrap of cloth simulating clothing." ^[20] One adult Ket, who had been careless with a cigarette, said, "It's a shame I don't have my doll. My house burnt down together with my dolls."^[21] Kets regard their dolls as household deities, which sleep in daytime and protect them at night.^[22]

For real continuity 24.000 years is maybe too long. But traditions and stories of Tasmanian aboriginals are remarkably similar to those on the mainland, even if they have been separated for 10.000 years.

 

[epoch]

By the way, the paper says that they identified (only) 0.9 ± 0.4% Neanderthal ancestry in K14, as opposed to 2.4% ± 0.4% in La Braña, and about 2% in modern Eurasians. They estimate the age of the Neandertal admixture at approx. 54,000 years ago (so most likely in the Middle East since Cro-Magnons had not yet reached Europe back then).

Ice man had far more.

http://johnhawks.net/weblog/reviews/neandertals/neandertal_dna/neandertal-ancestry-iced-2012.html

If we took as a baseline that Europeans have an average of 3.5 percent Neandertal, Ötzi would have around 5.5 percent (again, the actual percentage would be highly model-dependent). He has substantially greater sharing with Neandertals than any other recent person we have ever examined.