36,200YBP European genome

[Fire Haired14]

Genomic structure in Europeans dating back at least 36,200 years

Supplementary information

 

[motzart]

Thanks for posting! Super awesome find

It looks like he was Y DNA C along the same branch as La Brana. So Pre- C6?

Weird that this is showing up so much, what the heck does it represent.

 

[sparkey]

36,200YBP is a lower bound, with the upper bound being 38,700YBP. One old dude. Male, from European Russia, sample called Kostenki 14, or K14 for short. Y-DNA C.

 

[motzart]

The skull looks like Cro-Magnon

 

[sparkey]

Thanks for posting! Super awesome find

It looks like he was Y DNA C along the same branch as La Brana. So Pre- C6?

Weird that this is showing up so much, what the heck does it represent.

At first glance, I can't tell if they got a no-call or a negative call for V20, which would tell us if K14 is on the same branch as La Brana or not. The supplemental table for SNP calls isn't very helpful. Am I missing something? Anyway, I wouldn't be surprised if someone from so long ago carried proto-C-V20, in fact that may be the most likely possibility.

C-V20 seems to be a very old European lineage, I'd guess at least as old in Europe as Haplogroup I. It's still around, just very rare and a bit bottlenecked nowadays.

 

[sparkey]

mtDNA is U2 by the way, not particularly surprising.

 

[motzart]

At first glance, I can't tell if they got a no-call or a negative call for V20, which would tell us if K14 is on the same branch as La Brana or not. The supplemental table for SNP calls isn't very helpful. Am I missing something? Anyway, I wouldn't be surprised if someone from so long ago carried proto-C-V20, in fact that may be the most likely possibility.

C-V20 seems to be a very old European lineage, I'd guess at least as old in Europe as Haplogroup I. It's still around, just very rare and a bit bottlenecked nowadays.

For the data from (152) and (153), the informative SNPs are mutations on the branches of
the phylogenetic tree relating the individuals sequenced in the respective studies. They
therefore do not necessarily reflect diagnostic mutations for a particular haplogroup
defined in ISOGG. Nevertheless, they allow us to determine the likely branching point of
K14 simply by counting how often K14 matches the derived allele at each branch in the
tree. Results for both of theses datasets clearly show that K14 carries the derived alleles
for all SNPs on branches ancestral to hg C, but ancestral alleles for the branches leading
to more derived haplogroups (Fig. S13). Furthermore, K14 carries the derived allele for
four hg C mutations in ISOGG (P255, V183, V199, V232) (Table S6). The MHG
19
individual from La Braña (22) carries the same derived mutations, suggesting that both
are members of a closely related lineage within hg C.

 

[motzart]

I chopped out the K15

 

[bicicleur 2]

36,200YBP is a lower bound, with the upper bound being 38,700YBP. One old dude. Male, from European Russia, sample called Kostenki 14, or K14 for short. Y-DNA C.

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

which is this Kostenki?

 

[bicicleur 2]

different techno-complexes existed side by side in Kostenki
Aurignacian arrived 40000 years ago but there were allready modern humans in Kostenki before that
first modern humans at Kostenki probably arrived from Georgia, Aurignacian from the Balkans
was this individual Aurignacian ?
after my first read of the suplementary info, I have the impression he was not

 

[bicicleur 2]

For the data from (152) and (153), the informative SNPs are mutations on the branches of
the phylogenetic tree relating the individuals sequenced in the respective studies. They
therefore do not necessarily reflect diagnostic mutations for a particular haplogroup
defined in ISOGG. Nevertheless, they allow us to determine the likely branching point of
K14 simply by counting how often K14 matches the derived allele at each branch in the
tree. Results for both of theses datasets clearly show that K14 carries the derived alleles
for all SNPs on branches ancestral to hg C, but ancestral alleles for the branches leading
to more derived haplogroups (Fig. S13). Furthermore, K14 carries the derived allele for
four hg C mutations in ISOGG (P255, V183, V199, V232) (Table S6). The MHG
19
individual from La Braña (22) carries the same derived mutations, suggesting that both
are members of a closely related lineage within hg C.

what coverage do they have of this K14 individual?
it seems to me their coverage is not very high and they are not sure for the branches beyond C

 

[Maciamo]

I chopped out the K15

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.

 

[arvistro]

The three main matches are: Mesolithic European, Middle Eastern (Neolithic farmer) and South Asian.

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

 

[Angela]

Well, if this pans out in the long run, so much for all the disdain for Basal Eurasian because it was a late entrant from Africa into the holy precincts of the "Caucasian" world. Now, all of a sudden, eastern Europe was the refugia of Basal Eurasian and it didn't exist anywhere else. Am I the only one who finds these mental contortions so amusing? Good-bye, I guess, as well, to yDna "E" bringing it into the Levant very late from East or North Africa. Don't people keep track of how often they've been arrogantly wrong about so much? Apparently not.

On to more serious matters. I long ago speculated that since U2 has such a center of gravity in the Caucasus, the U2 in Kostenki very probably came from there. Now we are able to study his autosomes, and he is supposedly partly Basal Eurasian. It does all fit, if the data is being interpreted properly. I'm also reminded of all those old threads of Dienekes' talking about the Caucasus as the "Womb of Nations". I doubted it at the time, thinking that the Caucasus was more likely a refuge for defeated group after defeated group.

However, if Basal Eurasian spanned the Caucasus (we know it had to be south of the Caucasus as well, as the Neolithic farmers who set sail for Europe a la Paschou et al carried big doses of it) and then spread with the earliest farmers (and perhaps the Indo-Europeans) all the way west to the Atlantic, to India, south into Africa, and far north as well, then the general area could indeed be seen as the "Womb of Nations".

This is their "tree" by the way. Nice to see that there's at least general agreement with the Lazaridis et al tree. MHG seems to equal WHG, and NEOL seems to equal EEF. Was it really necessary to change the labels? Ego, ego, everywhere.
http://1.bp.blogspot.com/-jlF6eSOWmnk/VFwpvCk9MjI/AAAAAAAAJ1o/lkmfDp204OU/s1600/F2.large.jpg

Actually, however, I think a certain amount of caution is warranted. See Dienekes:
http://www.dienekes.blogspot.com/2014/11/genome-of-kostenki-14-upper-paleolithic.html

(This is the graphic he is discussing: http://www.sciencemag.org/content/early/2014/11/05/science.aaa0114/F1.large.jpg)

• The statistic D(Mbuti, East Asia; HG, K14) is less than 0. So, there's some link between HG and East Asians. Is this because of Basal Eurasian admixture in K14 or due to some admixture between Caucasoids and Mongoloids after the time of K14? (this might cause the lower dates of European-East Asian splits alluded to above).
• The statistic D(Mbuti, East Asia; NEOL, K14) is 0. So, East Asians don't "prefer" either Neolithic Europeans (NEOL) or K14. I guess the value of this statistic depends on how much Basal Eurasian the different populations have and what's the relationship between East Asians, K14, and the non-Basal Eurasian part in K14.
• Finally, "NEOL component for K14 in ADMIXTURE". I think they are referring to the "Middle East" component (right). This may be Basal Eurasian ancestry, or maybe because K14 is so old, it pre-dates the European/Middle Eastern divide and its ancestry isn't attracted to either Europe or the Middle East, so it gets ancestry from both (and many other colors besides)

I also think I want to wait and see whether the earliest Samara genomes contain any Basal Eurasian. What if Kostenki 14 was an autosomal dead end, as indeed is his mtDna? (So, although I am U2, I am not descended from him on my mtDna line.) There is also the expressed concern in the paper about possible "contamination" issues.

Also, we don't know where else Basal Eurasian was lurking during the UP and later on in time in the Mesolithic. If it made it over the Caucasus, what would have prevented it from crossing the Hellespont or sailing on a raft to the Aegean before farming ever developed? In that case, the incoming farmers from the Middle East would have been meeting long lost cousins.

We'll just have to wait and see. This is why this field of study never gets boring...endless surprises, and then, of course, there's the endless amusement provided by some of the more prolific writers on the subject. It's the gift that keeps on giving.

The clustering analysis in the graphic is also interesting. They divide the ancient samples into Hunter Gatherer, Middle East, Central Asia etc. By Middle East do they mean Basal Eurasian? They certainly are using Basal Eurasian as a category in other parts of the Supplement, so why didn't they divide it up that way for the cluster analysis? Or are they using it to mean Neolithic farmer? That doesn't seem right, either. I'm still plowing through the Supplement. If someone can find text to that effect that would be helpful.

It's worthy of note, I think, that they find African in Ajv 58 and La Brana (as did the Dodecad analyses), as well as a smidgeon in Motala. (This is why admixture analyses that scrub European genomes of anything which they conveniently label "noise" are so unhelpful, by the way.) Interestingly, there is none or at least barely a trace in Stuttgart or Otzi (although I think Dodecad found some), so did the African they found in the Gok sample mostly come from the additional HG? I do hate to say I told you so, but it also seems from this analysis that North Italians carry a substantial UP remnant in their genomes, although not as high as that of the French or the French Basues. I knew that all those "CM" phenotypes couldn't be totally unrelated to genotype, even if it's not a perfect correlation, and nor could they all have been brought in by the Indo-Europeans.

 

[Maciamo]

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

We are talking about genetic similarities here, not direct ancestry or descent.

 

[Maciamo]

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).

 

[ElHorsto]

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.

 

[ElHorsto]

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).

I saw this post right after I wrote mine. It reads like my thoughts.

 

[ElHorsto]

I do hate to say I told you so, but it also seems from this analysis that North Italians carry a substantial UP remnant in their genomes, although not as high as that of the French or the French Basues. I knew that all those "CM" phenotypes couldn't be totally unrelated to genotype, even if it's not a perfect correlation, and nor could they all have been brought in by the Indo-Europeans.

I agree with that, provided I understand you correctly. Many seem to forget that Cro-Magnon is one particular find which is presumably 28000 years old, old enough to share more common ancestry with both, HG and Farmers, than later more differentiated peoples. The "CM" phenotype refers to this original Cro-Magnon find only, but unfortunately it has become popular to call all pre-neolithic europeans "Cro-Magnons", which leads to confusion with the particular Cro-Magnon phenotype.

 

[Angela]

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).

I agree with that. That's why I think it's much more informative to see how much ANE is in a population than trying to break ANE down into populations that didn't exist at the time that he lived. The same goes for WHG and EEF. In the case of ANE, for example, who says that his "admixture" results don't just show the flow of his genome into all those populations?