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Fire Haired14
07-11-14, 01:38
Genomic structure in Europeans dating back at least 36,200 years (http://www.sciencemag.org/content/early/2014/11/05/science.aaa0114)

Supplementary information (http://www.sciencemag.org/content/suppl/2014/11/05/science.aaa0114.DC1/Seguin-Orlando.SM.pdf)

motzart
07-11-14, 01:55
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
07-11-14, 01:56
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
07-11-14, 02:03
The skull looks like Cro-Magnon

http://i.imgur.com/e3ODI7A.jpg

sparkey
07-11-14, 02:03
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
07-11-14, 02:10
mtDNA is U2 by the way, not particularly surprising.

motzart
07-11-14, 02:21
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
07-11-14, 02:22
I chopped out the K15

http://i.imgur.com/KKdHayp.png

bicicleur
07-11-14, 10:12
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
07-11-14, 11:05
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
07-11-14, 11:10
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
07-11-14, 12:59
I chopped out the K15

http://i.imgur.com/KKdHayp.png

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
07-11-14, 13:18
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
07-11-14, 17:12
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
07-11-14, 18:30
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
07-11-14, 18:51
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
07-11-14, 18:58
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
07-11-14, 19:01
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
07-11-14, 19:15
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
07-11-14, 19:24
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?

Greying Wanderer
07-11-14, 20:19
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
07-11-14, 20:22
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
07-11-14, 21:54
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
07-11-14, 22:13
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
07-11-14, 22:31
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
07-11-14, 22:47
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
07-11-14, 23:04
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
08-11-14, 02:12
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
08-11-14, 11:03
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
08-11-14, 12:20
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
08-11-14, 16:29
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/archaeology/2014/11/european-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
08-11-14, 16:48
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
08-11-14, 19:22
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
08-11-14, 21:09
"“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
08-11-14, 21:20
deleted - rethinking the idea

Angela
08-11-14, 21:38
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
08-11-14, 21:51
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

http://i.imgur.com/3aX0H7o.jpg

epoch
09-11-14, 09:18
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/%D1%81%D1%80%D0%B0%D0%B2%D0%BD%D0%B5%D0%BD%D0%B8%D 0%B5-%D0%B4%D0%B2%D1%83%D1%85-%D0%B4%D1%80%D0%B5%D0%B2%D0%BD%D0%B8%D1%85-%D0%B5%D0%B2%D1%80%D0%BE%D0%BF%D0%B5%D0%B9%D1%86%D 0%B5%D0%B2-%D0%B8-%D0%BE/

epoch
09-11-14, 09:38
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] (http://en.wikipedia.org/wiki/Ket_people#cite_note-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] (http://en.wikipedia.org/wiki/Ket_people#cite_note-21) Kets regard their dolls as household deities (http://en.wikipedia.org/wiki/Household_deity), which sleep in daytime and protect them at night.[22] (http://en.wikipedia.org/wiki/Ket_people#cite_note-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
09-11-14, 10:31
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.

motzart
09-11-14, 17:27
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 think they do the admixtures backwards too, rather than showing the ancestral genomes as a composition of modern genomes they should show the ancestral genome as homogenous and measure its contribution to modern populations. It seems to me to make a lot more sense to say that Ust Ishim or K14 left little contributions to a wide variety of modern populations than to say he was most closely related to some modern group. Considering descendants of Y DNA K are widespread in Asia it would make logical sense to see the original K group diffused into many genetically different pre-existing Asian groups and making contributions to each relative to their size.

For Neanderthal ancestry it seems like it is vastly underestimated. They make the Neanderthal ancestry judgement based on the (single?) genome of an Altai Neanderthal, considering Neanderthals had been around for hundreds of thousands of years they had to be a diverse group so making that judgement based on one genome seems wrong.

Angela
09-11-14, 18:37
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


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.

Very interesting. Thanks. I wonder if the Lares and Penates might be related to this?

http://archaeologicalmuseum.jhu.edu/wp-content/uploads/2013/04/NWK4337web.jpg

By the way, this is the Venus from the Grimaldi cave:
http://media-cache-ak0.pinimg.com/236x/2c/9b/48/2c9b4887ee8f2c4fdb4ccc9485d73978.jpg

And, of course, sculptors are still at it. This is Henry Moore's version of the Magna Mater:
http://media-cache-ec0.pinimg.com/236x/27/56/85/275685be779aef24e2601ed7250b6904.jpg

LeBrok
09-11-14, 23:57
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.
You are correct. It is impossible to recover 100% DNA from ancient bones, and further back you go the smaller it gets. For example in this research, table on page 3 (http://www.nature.com/ncomms/2014/141021/ncomms6257/pdf/ncomms6257.pdf), look for Mean Coverage. Numbers bigger than 7 might mean almost full genome, less than 1 mean very small sections recovered. It is hard to find info about number of base pairs of the dna recovered, which would give us full picture.
More info about coverage of genome: https://www.broadinstitute.org/crd/wiki/index.php/Read_coverage

Here is a paragraph from related paper, how hard it is to recover ancient dna and keep it clean from bacterial and living human dna (researchers' dna), remove errors due to shotgun technique and due to dna degeneration since death of individual:


Finally, to further test whether our initial assumption that sequencing errors are
randomly distributed across the genome, we compared the coordinates of our 161
candidate regions with a list of ~400,000 genomic locations where duplicate Illumina
whole-genome sequence data from the same individual had discrepant genotype calls
(without standard filters and with a genotype quality cutoff of GQ ≥ 20; cf. (175)). We
filtered out all candidate regions that contained one or more of these discrepant genotype
calls. 121 regions failed this filter, with each containing an average of 97 discrepant
genotype calls (null expectation of random locations for these Illumina sequencing errors
would lead to ~1.2 per region). This left 40 candidates for ancient introgression, with an
average length of 6.0 Kb. Given the uncertainty in our assumptions regarding the
baseline distributions of sequencing errors and post-mortem DNA damage, and the small
size of the identified regions, we do not believe these observations are necessarily
inconsistent with a null model of no admixture.

LeBrok
10-11-14, 00:23
"“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.

I think, on a scale of tens and hundreds of years people didn't mix much, as naturally they stick to their own culture, language and religion and prefer to stay separated from others. On scale of thousands of years many mixing events will happen, either migrations, conquests, or even slow but steady and cumulative gene flow.

The slow, rare mixing is interesting though. Your mathematical formula makes lot of sense in a scenario where all genes are equal on selective level. However in cases of very positive mutations, their flow from other tribes will be accelerated or even explosive. This will surely increase transfer of the rest of the genome of the founder of positive mutation. Other words, some admixture can piggyback on a positive mutation.

Greying Wanderer
10-11-14, 06:17
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


The placing of the (small) hands over the stomach strikes me as being surprisingly consistent.

I'd guess the heads/legs often broke off over time.

Greying Wanderer
10-11-14, 06:19
I think, on a scale of tens and hundreds of years people didn't mix much, as naturally they stick to their own culture, language and religion and prefer to stay separated from others. On scale of thousands of years many mixing events will happen, either migrations, conquests, or even slow but steady and cumulative gene flow.

The slow, rare mixing is interesting though. Your mathematical formula makes lot of sense in a scenario where all genes are equal on selective level. However in cases of very positive mutations, their flow from other tribes will be accelerated or even explosive. This will surely increase transfer of the rest of the genome of the founder of positive mutation. Other words, some admixture can piggyback on a positive mutation.

good point

Greying Wanderer
10-11-14, 06:21
I think they do the admixtures backwards too, rather than showing the ancestral genomes as a composition of modern genomes they should show the ancestral genome as homogenous and measure its contribution to modern populations. It seems to me to make a lot more sense to say that Ust Ishim or K14 left little contributions to a wide variety of modern populations than to say he was most closely related to some modern group. Considering descendants of Y DNA K are widespread in Asia it would make logical sense to see the original K group diffused into many genetically different pre-existing Asian groups and making contributions to each relative to their size.

For Neanderthal ancestry it seems like it is vastly underestimated. They make the Neanderthal ancestry judgement based on the (single?) genome of an Altai Neanderthal, considering Neanderthals had been around for hundreds of thousands of years they had to be a diverse group so making that judgement based on one genome seems wrong.

Especially if there was more than one archaic involved.

arvistro
10-11-14, 08:25
There are statements like:
Every Human being shares 99% of its genome. Or more catchy about humans sharing 50% of genes with banana thing.
Now we are talking about say few % of Neanderthal in humans. Obviously there is a big gap between these 2 concepts. Can anyone suggest me a good read to catch up? Preferrably sort of idiot's guide.

LeBrok
10-11-14, 18:21
There are statements like:
Every Human being shares 99% of its genome. Or more catchy about humans sharing 50% of genes with banana thing.
Now we are talking about say few % of Neanderthal in humans. Obviously there is a big gap between these 2 concepts. Can anyone suggest me a good read to catch up? Preferrably sort of idiot's guide.
I never found well written explanation about this kind of discrepancies. If people are 99.999% genetically similar, why am I only 50% like my mother and 4% like my cousin?
What I managed to gather through years, is that it all depends on resolution of genetic similarities. If we compare only genetic functions, regardless if genes, more precisely alleles (mutations of single letters) are identical, we will get very close relationships between banana, chimp and human. We have same genes, meaning genes that perform same functions.
When we increase resolution of comparison, and starting comparing genes, the alleles, to the single letters, similarities starting to drop dramatically. We might have 0% exact matches to banana, 0.5% with chimps, 4% cousins and 50% with mother.
With less resolution we are talking about genetic similarities. With more resolution we are talking about exact matching alleles.

Comparison with Neanderthal is still a bit different animal, so to speak. For this, I think, we need modern African and European genome and Neanderthal one. Then we compare genes of an European to other two, checking one by one which gene is more like Europeans. They won't match exactly to the letter, because of recent mutations from the time we all separated, but most important is which ones are more similar. More similar means more closely related.
In this case about 2.5% genes of single European resemble Neandertal alleles the most. Well, that's my guess how it is done.

LeBrok
10-11-14, 18:44
You are correct. It is impossible to recover 100% DNA from ancient bones, and further back you go the smaller it gets. For example in this research, table on page 3 (http://www.nature.com/ncomms/2014/141021/ncomms6257/pdf/ncomms6257.pdf), look for Mean Coverage. Numbers bigger than 7 might mean almost full genome, less than 1 mean very small sections recovered. It is hard to find info about number of base pairs of the dna recovered, which would give us full picture.
More info about coverage of genome: https://www.broadinstitute.org/crd/wiki/index.php/Read_coverage

Here is a paragraph from related paper, how hard it is to recover ancient dna and keep it clean from bacterial and living human dna (researchers' dna), remove errors due to shotgun technique and due to dna degeneration since death of individual:

Adding some more.

http://www.eva.mpg.de/neandertal/index.html

DNA sequences were generated on the Illumina HiSeq platform and constitute an average 50-fold coverage of the genome. 99.9% of the 1.7GB of uniquely mappable DNA sequences in the human genome are covered at least ten times.
What exactly does it mean? Expert opinion very welcome!

What I think it means:
1. They "covered", produced enough DNA (through multiplication/copying of DNA) to run their full tests 50 times.
2. 50 runs are enough to cover whole human genome 10 times.
3. "99.9% Uniquely mappable" means without mistakes, exact matches.

At first glance "99.9% of the 1.7GB of uniquely mappable DNA sequences in the human genome" seems like they recovered 99.9% of full genome, but is it the case? Perhaps it means that whatever they recovered they could read with 99.9% precision?

However, they had run the test 50 times, if enough genetic material was collected, they should have been able to reconstruct the full DNA.
I think that they are not sure about how close to the whole genome they got, that's why the wording is not direct, like " we recovered" 99.9% of genome".

epoch
11-11-14, 23:50
The IBD map of Ust-Ishim.

http://s017.radikal.ru/i438/1411/5a/a06eaaddfbd8.png

The links with Saami and Estonians is clear. The link with Siberians is clear. The very slight link with French and Italians is interesting. The Bulgarian uptick is interesting. Does this seem related to Y-DNA N? Not everywhere, but it seems related nevertheless. It also seems related to Turkics

http://en.wikipedia.org/wiki/Y-DNA_haplogroups_in_Central_and_North_Asian_populat ions
http://www.eupedia.com/europe/european_y-dna_haplogroups.shtml (http://en.wikipedia.org/wiki/Y-DNA_haplogroups_in_Central_and_North_Asian_populat ions)

Alan
12-11-14, 00:05
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/%D1%81%D1%80%D0%B0%D0%B2%D0%BD%D0%B5%D0%BD%D0%B8%D 0%B5-%D0%B4%D0%B2%D1%83%D1%85-%D0%B4%D1%80%D0%B5%D0%B2%D0%BD%D0%B8%D1%85-%D0%B5%D0%B2%D1%80%D0%BE%D0%BF%D0%B5%D0%B9%D1%86%D 0%B5%D0%B2-%D0%B8-%D0%BE/

It is not only not good, the coloring/shading is so completely wrong.


Just as example

Russian ~20%
Swedish~18%
French ~13,5%
Lezgian ~27%
Iranian = ~19,5%
Turkish = ~16%
Kurdish= ~18%
Tadjik = ~28%
Pathan = ~32.5%
Krygyz = ~18%
Italian = ~10%
Polish = ~19%


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


Now compare these results with the map.

JS Bach
12-11-14, 03:23
From what I gather, the IBD map may well be more accurate, but I think the admixture calculators are also interesting. In Eurogenes15 it breaks down as:



Population



North_Sea
-


Atlantic
11.24%


Baltic
-


Eastern_Euro
3.08%


West_Med
4.82%


West_Asian
-


East_Med
-


Red_Sea
3.36%


South_Asian
30.76%


Southeast_Asian
15.25%


Siberian
2.02%


Amerindian
2.20%


Oceanian
10.96%


Northeast_African
10.08%


Sub-Saharan
6.22%



Of note, he has 11.24% Atlantic, but has none of the North_Sea, Baltic, West_Asian or East_Med components. I wonder how it got the extreme West Eurasian Atlantic component, but missed those North European, Caucasian and Near Eastern components? Could it be that Y-dna R perhaps made it to the Basque region early? I've noticed in runs of Eurogenes15 with other Ancient dna that the Atlantic component is a popular component, suggesting it's been there for a while. If it's related to Y-dna I then how come the Y-dna J-heavy Caucasian and Near Eastern components are zero? Or maybe it's related to Y-dna C, which might have piggy-backed on Y-dna K and then had a branch go over to where La Brana was? Or maybe it's a Solutrean Q? Who knows?

JS Bach
12-11-14, 07:33
Looking at some ancient genomes through Eurogenes15, it's striking how Mal'ta lacks the Atlantic component that Ust'-Ishim has:



Eurogenes15
Ust'-Ishim (http://www.y-str.org/2014/11/ust-ishim-ancient-dna.html)
Mal'ta


North_Sea
-
15.91%


Atlantic
11.24%
-


Baltic
-
6.54%


Eastern_Euro
3.08%
38.02%


West_Med
4.82%
-


West_Asian
-
-


East_Med
-
-


Red_Sea
3.36%
-


South_Asian
30.76%
20.31%


Southeast_Asian
15.25%
-


Siberian
2.02%
-


Amerindian
2.20%
18.62%


Oceanian
10.96%
0.12%


Northeast_African
10.08%
-


Sub-Saharan
6.22%
0.47%



Seeing as Mal'ta was Y-dna R, this leads me away from thinking the Atlantic component is associated with R. Although I understand how weak correlations between uni-parental and autosomal markers are these days, maybe in ancient times those associations were stronger.

Alan
12-11-14, 14:37
Looking at some ancient genomes through Eurogenes15, it's striking how Mal'ta lacks the Atlantic component that Ust'-Ishim has:



Eurogenes15
Ust'-Ishim (http://www.y-str.org/2014/11/ust-ishim-ancient-dna.html)
Mal'ta


North_Sea
-
15.91%


Atlantic
11.24%
-


Baltic
-
6.54%


Eastern_Euro
3.08%
38.02%


West_Med
4.82%
-


West_Asian
-
-


East_Med
-
-


Red_Sea
3.36%
-


South_Asian
30.76%
20.31%


Southeast_Asian
15.25%
-


Siberian
2.02%
-


Amerindian
2.20%
18.62%


Oceanian
10.96%
0.12%


Northeast_African
10.08%
-


Sub-Saharan
6.22%
0.47%



Seeing as Mal'ta was Y-dna R, this leads me away from thinking the Atlantic component is associated with R. Although I understand how weak correlations between uni-parental and autosomal markers are these days, maybe in ancient times those associations were stronger.

In this calculator most of the Gedrosia get eaten up by "South Asian" and Caucasus by "Eastern Euro" I remember very well.

LeBrok
12-11-14, 18:34
Interesting. They really went separate ways, only mating together in South Asia.

epoch
12-11-14, 21:49
@Alan

That was an IBD map, not just ANE admixture. IBD's are series of SNP's, each in itself not necessarily unique to an admixture, recognizable in offspring. The order is what makes them unique, if I understand it all well, not the mutations of drifts. IBD should be markers of decent.

http://en.wikipedia.org/wiki/Identity_by_descent

Could the difference be that the original ANE population was far larger than the tribe the Mal'ta boy lived in?

ElHorsto
13-11-14, 01:06
@Alan

That was an IBD map, not just ANE admixture. IBD's are series of SNP's, each in itself not necessarily unique to an admixture, recognizable in offspring. The order is what makes them unique, if I understand it all well, not the mutations of drifts. IBD should be markers of decent.

http://en.wikipedia.org/wiki/Identity_by_descent

Could the difference be that the original ANE population was far larger than the tribe the Mal'ta boy lived in?

I think you are right. IBD patterns are more fragile, somewhat like haplogroups, while admixtures are more robust by relying on independent SNP's and are thus more continuously distributed. Thus ANE admixture could have been much more widespread than the Mal'ta tribe already back then.

Greying Wanderer
13-11-14, 02:45
From what I gather, the IBD map may well be more accurate, but I think the admixture calculators are also interesting. In Eurogenes15 it breaks down as:



Population



North_Sea
-


Atlantic
11.24%


Baltic
-


Eastern_Euro
3.08%


West_Med
4.82%


West_Asian
-


East_Med
-


Red_Sea
3.36%


South_Asian
30.76%


Southeast_Asian
15.25%


Siberian
2.02%


Amerindian
2.20%


Oceanian
10.96%


Northeast_African
10.08%


Sub-Saharan
6.22%



Of note, he has 11.24% Atlantic, but has none of the North_Sea, Baltic, West_Asian or East_Med components. I wonder how it got the extreme West Eurasian Atlantic component, but missed those North European, Caucasian and Near Eastern components? Could it be that Y-dna R perhaps made it to the Basque region early? I've noticed in runs of Eurogenes15 with other Ancient dna that the Atlantic component is a popular component, suggesting it's been there for a while. If it's related to Y-dna I then how come the Y-dna J-heavy Caucasian and Near Eastern components are zero? Or maybe it's related to Y-dna C, which might have piggy-backed on Y-dna K and then had a branch go over to where La Brana was? Or maybe it's a Solutrean Q? Who knows?

I tend to think it's layers of expansions with later ones largely but not completely covering over the earlier ones leaving behind a collection of autosomal signals from each layer, particularly in refuge zones.

So in my model I imagine a population coming out of the African tropical zone into the rest of Africa and across Eurasia, coastal dominated. So that's the first layer, layer B.

Then somewhere within its range (S/SE Asia maybe) a segment of the B population develops a major advantage of some kind becoming population C and that population then expands out from its source region *over the top* of the B layer.

So now you have a C layer over most of the globe with B mostly surviving as an autosomal component within C. The proportion that survives varies from place to place with higher quantities in certain refuge zones (mountains, swamps etc).

If that was correct then it seems plausible to me that if the C layer was out of S/SE Asia then the B layer might have survived best in refuge zones in the farthest periphery e.g. the Atlantic coast. These zones might include mountainous areas along the coast like Atlantic Iberia or Brittany but might include bits of the Baltic coast also. This above average underlying signal would pull out the "Atlantic" component.

So in this model Ust-Ishim would represent a part of the C layer population with a higher than average amount of the B layer.

(This would explain the very high S/SE Asian/Oceanian components (the C layer) with Atlantic (above average amount of the B layer.)

(This would imply the "North European" and "Caucasian/Near Eastern/West Asian" components were other separate layers - possibly connected to I and J in some way.)

.

The combination of the B and C layers might then create two "basal" signals: a widespread one where the C layer is dominant and there is only a small autosomal B signal and a more western coastal orientated basal where the B layer is a significant component.

The test would be looking for a slightly different "basal" along the Atlantic coast and maybe parts of the med. coast also.)

Angela
13-11-14, 02:55
I don't know if everyone has seen Martin Sikorra's post on Razib Khan's blog. He's one of the study authors.

http://www.unz.com/gnxp/

Hi Razib,
after reading your post it I thought it would not hurt to chime in with a bit of perspective from my side, as I don’t entirely agree with some of your criticisms. Some of the reactions to our paper have caught me a little by surprise, but in retrospect it probably reflects the complexity of the story, which is something I also struggled with (and still am!).

Part of the confusion seems to be that it is assumed that since we find that K14 somehow relates to all three European ancestral proposed by Lazaridis et al., that it necessarily also has contributed these components to modern Europeans. In your post you also seem to imply that, i.e we don’t “acknowledge the possibility that K14 did not leave modern descendants, and was part of an early population which did not end up flourishing”. I actually agree with the early population part, and we also acknowledge that in our suggested model in Figure 2, which does not have a K14-related population directly contributing to modern Europeans. What one can say with reasonable certainty though is that K14 does share substantial amount of ancestry with Mesolithic Hunter-gatherers (and therefore modern Europeans by extension), but at the same time appears less close to East Asians than all Western Eurasians, so things are complex.

Therefore if you take the Lazaridis et al. model as a backbone, you need some extra gene flow to account for that, be it from Basal Eurasian into K14, or some sort of basal gene flow between East Asia and early West Eurasians, post-K14 but pre-ANE/HG split. While we don’t have the resolution to be sure, our results do suggest that K14 was close to or a already somewhat down the HG branch of the ANE/HG split, which implies that those proposed components would not only have to be already somewhat differentiated by 36 kya, but also already have had mixed to a certain extent.

Regarding your take on the PCA results, I would disagree and say that these are very much what you would expect for an individual of that age. K14 is after all ~36,000 years closer to the East Asia / West Eurasia split, so it lacks a substantial amount of drift on the European branch. It is nevertheless shifted towards Europe on PC1 from the origin as expected (a bit more so than MA1 actually). Pontus Skoglund had a nice recent paper in MBE that demonstrates the same effect (see Figure 9 in doi:10.1093/molbev/msu1920). As you say, using modern variation to infer affinities of ancient samples has limitations, and PCs are often hard to interpret. In the same spirit I would also not interpret the different admixture components in K14 as itself being admixed with all those components, but rather reflecting ancestral relationship with modern populations represented by these components. The same is obviously true for the “Middle East” component, but it still implies that K14 somehow relates ancestrally to those populations whereas all other HGs including MA1 do not.

Overall, I do think that migrations played an important role, e.g. I don’t think that “Basal Eurasian” came with K14 to Central Europe or was already present back then in another way, that seems pretty clear. I would also not say that our results are necessarily a refutation of the Lazaridis et al model, but I do think they show that it seems to have been already quite complicated in the Upper Paleolithic. If you need a new migration/component for every new individual, to me this questions at least to a some extent whether one can really talk about three or any other number of discrete ancestral populations for all modern Europeans. Personally I would expect ancient samples from the Caucasus or Central Asia to yet again spring some surprises. The cool thing is that we’ll probably know soon, since many groups are adding more and more samples to the picture.
Anyways, I just wanted to share my thoughts, hope this clears up things a bit.

Btw regrading your subsequent ANE post, I can confirm that those are the Kalash. Interesting also that the correspondingly the Kalash ADMIXTURE component shows up in MA1, but is almost absent in K14 (see our Figure S20).

Greying Wanderer
13-11-14, 04:39
"I would also not say that our results are necessarily a refutation of the Lazaridis et al model, but I do think they show that it seems to have been already quite complicated in the Upper Paleolithic."

Incoming theory, skip if annoying

If the process is one where a population develops an advantage and expands from a source region and then one segment of that expanded population then develops a further advantage and expands back over the top of the previous layer in a sequence of population layers building up a bit like sedimentary rocks then say for the sake of argument this process could be modeled as:

the previous layer becomes 20% of the combined autosomal

then the sequence would go something like

1st layer A
A 100%

2nd layer B
A 20%
B 80%

3rd layer C
A 4%
B 16%
C 80%

4th layer D
A 0.8%
B 3.2%
C 16%
D 80%

As the layers build up the earliest layers become compressed and also relatively closer to each other compared with the later layers. So I wonder if something like that is effecting basal i.e. it's a collection of similar small signals rather than one signal, so in the example components A and B are two separate components of 0.8% and 3.2% but mostly register as a single layer AB of 4%.

Except in a few places where the A is bigger - say the model is modified to say that in refuge zones 40% of the previous layer is preserved instead of just 20% in which case it goes:

A 100%

A 40%
B 60%

A 16%
B 24%
C 60%

A 6.4%
B 9.6%
C 24%
D 60%

so the A is big enough to notice.

Something like that anyway.

Aberdeen
13-11-14, 04:58
I have some concerns that the way this paper is referring to basal Eurasians possibly involves a misunderstanding of what Lazardis et al meant when they referred to basal Eurasians as forming at least 44% of EEF. Based on what the word "basal" means, I can understand why there's an assumption in this paper that basal Eurasians are those Eurasians who existed before the split occurred in the out of Africa population in the Middle East. However, when I look at the paper on the three founding populations of Europe, it seems to refer to a population that split off from the original out of Africa group and evolved into something separate perhaps in Saudia Arabia and perhaps as a result of further gene flow from East Africa, so Lazardis's basal Eurasians who mixed with some other group (perhaps Balkan hunter gatherers) to become EEF were different from the original out of Africa group. Am I misunderstanding the issue? I don't see how the group that Lazardis considers to be Middle Eastern farmers who mixed with other populations as it flowed into Europe could have existed 36,000 years ago.

epoch
13-11-14, 21:59
I think you are right. IBD patterns are more fragile, somewhat like haplogroups, while admixtures are more robust by relying on independent SNP's and are thus more continuously distributed. Thus ANE admixture could have been much more widespread than the Mal'ta tribe already back then.

Stretching from Lake Baikal to SHG's perhaps? Motola had 19% ANE and Mal'ta 58% IIRC. I would love to see the IBD map of Motola.

Another thing: Motola was considered part of a population that was replaced according to Skoglund, yet current day Swedes have substantial ANE and WHG. Ust-Ist had a substantial amount of ENA, a small amount of North-Euro, just as current Siberians, and John Hawks consideres him ancestral to no known population and now we have K14, which also shows admixture that can be found in the current population in the same area and yet again everybody considers it ancestral to nobody.

We obviously have more finds (Mal'ta with no East-Asian, WHG with no Basal or ANE) but if these were the only finds we had we would have thought that the case for continuity was made.

Mind you, I don't think anything is proven here. It just struck me as odd that those that show similarity to present day people are considered dead-ends.

epoch
13-11-14, 23:08
@Angela

In that ANE post Martin Sikorra mentions Razib states the following:


Recall that the highest fraction of Ancestral North Eurasia (ANE) outside of the New World is among the peoples of the North Caucasus. Their shared drift statistic is depressed in comparison to Europeans because of their high fraction of Basal Eurasians (BEu)

http://www.unz.com/gnxp/ancestral-north-eurasians-about-the-world/

Why do Caucasians (The region, not the American term for whites) have such high Basal Eurasian component?

Angela
14-11-14, 00:14
@Angela

In that ANE post Martin Sikorra mentions Razib states the following:



http://www.unz.com/gnxp/ancestral-north-eurasians-about-the-world/

Why do Caucasians (The region, not the American term for whites) have such high Basal Eurasian component?

Going back to Dienekes' exercise where he descirbes the various Dodecad components in terms of one another, in the blog about K12b in terms of World 9, southwest Asian = Caucasus. Caucasus is Atlantic Med plus Gedroisia, plus slices of southwest Asian and Northwest African.

http://dienekes.blogspot.com/2012/08/inter-relationships-of-dodecad-k12b-and.html

When he examines the K7b and K12b components in terms of one another, Caucasus shows up as about 1/3 "Southern" (I wonder if that would get closer to Basal or at least to ancient Near Eastern) a small slice of Atlantic Med, and almost 2/3 going to "West Asian", which in these analyses is just Caucasus with a big slice of Gedrosia.

http://dienekes.blogspot.com/2012/09/inter-relationships-between-dodecad-k7b.html

So, to address your question, don't Caucasians show such a large amount of Basal Eurasian because Caucasians are a mix of mostly farmer (ancient Near Eastern) ancestry with a big dollop of ANE?

If his analysis of the age of these components is pretty accurate, then "Caucasus" as a component is pretty old, certainly older than East African or even Atlantic Baltic.

JS Bach
14-11-14, 01:02
Interesting comments. Here are the Eurogenes15, Dodecad12b, and DodecadV3 results for Ust' Ishim, Kostenki14 and Mal'ta:



Eurogenes15
Ust'-Ishim (http://www.y-str.org/2014/11/ust-ishim-ancient-dna.html)
Kostenki
14
Mal'ta

Dodecad K12b
Ust'-Ishim (http://www.y-str.org/2014/11/ust-ishim-ancient-dna.html)
Kostenki
14
Mal'ta

Dodecad V3
Ust'-Ishim (http://www.y-str.org/2014/11/ust-ishim-ancient-dna.html)
Kostenki
14
Mal'ta


North_Sea
-
18.81%
15.91%

Gedrosia
9.58%
12.38%
24.39%

East_European
4.55%
11.89%
20.03%


Atlantic
11.24%
12.39%
-

Siberian
2.70%
3.78%
13.55%

West_European
8.95%
30.62%
37.68%


Baltic
-
6.52%
6.54%

Northwest_African
2.58%
1.65%
-

Mediterranean
4.94%
15.55%
-


Eastern_Euro
3.08%
9.71%
38.02%

Southeast_Asian
13.76%
6.12%
-

Neo_African
3.76%
1.43%
0.38%


West_Med
4.82%
9.77%
-

Atlantic_Med
6.82%
21.46%
-

West_Asian
-
0.63%
-


West_Asian
-
-
-

North_European
7.39%
28.80%
47.46%

South_Asian
30.85%
17.75%
26.04%


East_Med
-
-
-

South_Asian
31.50%
15.70%
14.36%

Northeast_Asian
5.96%
4.58%
15.53%


Red_Sea
3.36%
5.70%
-

East_African
8.24%
3.87%
-

Southeast_Asian
21.76%
6.72%
-


South_Asian
30.76%
17.42%
20.31%

Southwest_Asian
3.36%
4.95%
-

East_African
7.03%
1.92%
-


Southeast_Asian
15.25%
1.33%
-

East_Asian
8.40%
0.15%
-

Southwest_Asian
3.86%
4.61%
-


Siberian
2.02%
0.66%
-

Caucasus
-
-
-

Northwest_African
3.25%
2.07%
-


Amerindian
2.20%
4.74%
18.62%

Sub_Saharan
5.67%
1.15%
0.24%

Palaeo_African
5.10%
2.24%
0.34%


Oceanian
10.96%
5.11%
0.12%












Northeast_African
10.08%
5.19%
-











Sub-Saharan
6.22%
2.66%
0.47%











None of them have the K12b Caucasus component, or the Eurogenes15 West_Asian or East_Med components, and Kostenki14 has just 0.63% of the West_Asian component in Dodecad V3.

My first thought when seeing the Eurogenes15 results for Kostenki14 was that it was contamination, but now seeing how they all lack that Caucasus / Near Eastern component makes me think it is the real deal. Why it's missing that area, and seeing how Kostenki14 is so close to there geographically though is intriguing.

MOESAN
14-11-14, 01:25
"“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.

I agree for the most - but even nomadic populations could have had a high enough endogamy deportment - it depends on size of clan I suppose, the smallest the less regardant for strangers?

MOESAN
14-11-14, 01:29
to EPOCH
the link with Y-N is not evident - these regions were run also by Y-C (the supposed SNP of this man) and later by Y-R* bearers too -
keep in mind Y-N1 is not so old in Finland Estonia (Bronze Age?)

Greying Wanderer
14-11-14, 04:35
I agree for the most - but even nomadic populations could have had a high enough endogamy deportment - it depends on size of clan I suppose, the smallest the less regardant for strangers?

Yes, nomadic + too small for endogamy to be a viable option.

Greying Wanderer
14-11-14, 04:37
Interesting comments. Here are the Eurogenes15, Dodecad12b, and DodecadV3 results for Ust' Ishim, Kostenki14 and Mal'ta:



Eurogenes15
Ust'-Ishim (http://www.y-str.org/2014/11/ust-ishim-ancient-dna.html)
Kostenki
14
Mal'ta

Dodecad K12b
Ust'-Ishim (http://www.y-str.org/2014/11/ust-ishim-ancient-dna.html)
Kostenki
14
Mal'ta

Dodecad V3
Ust'-Ishim (http://www.y-str.org/2014/11/ust-ishim-ancient-dna.html)
Kostenki
14
Mal'ta


North_Sea
-
18.81%
15.91%

Gedrosia
9.58%
12.38%
24.39%

East_European
4.55%
11.89%
20.03%


Atlantic
11.24%
12.39%
-

Siberian
2.70%
3.78%
13.55%

West_European
8.95%
30.62%
37.68%


Baltic
-
6.52%
6.54%

Northwest_African
2.58%
1.65%
-

Mediterranean
4.94%
15.55%
-


Eastern_Euro
3.08%
9.71%
38.02%

Southeast_Asian
13.76%
6.12%
-

Neo_African
3.76%
1.43%
0.38%


West_Med
4.82%
9.77%
-

Atlantic_Med
6.82%
21.46%
-

West_Asian
-
0.63%
-


West_Asian
-
-
-

North_European
7.39%
28.80%
47.46%

South_Asian
30.85%
17.75%
26.04%


East_Med
-
-
-

South_Asian
31.50%
15.70%
14.36%

Northeast_Asian
5.96%
4.58%
15.53%


Red_Sea
3.36%
5.70%
-

East_African
8.24%
3.87%
-

Southeast_Asian
21.76%
6.72%
-


South_Asian
30.76%
17.42%
20.31%

Southwest_Asian
3.36%
4.95%
-

East_African
7.03%
1.92%
-


Southeast_Asian
15.25%
1.33%
-

East_Asian
8.40%
0.15%
-

Southwest_Asian
3.86%
4.61%
-


Siberian
2.02%
0.66%
-

Caucasus
-
-
-

Northwest_African
3.25%
2.07%
-


Amerindian
2.20%
4.74%
18.62%

Sub_Saharan
5.67%
1.15%
0.24%

Palaeo_African
5.10%
2.24%
0.34%


Oceanian
10.96%
5.11%
0.12%












Northeast_African
10.08%
5.19%
-











Sub-Saharan
6.22%
2.66%
0.47%











None of them have the K12b Caucasus component, or the Eurogenes15 West_Asian or East_Med components, and Kostenki14 has just 0.63% of the West_Asian component in Dodecad V3.

My first thought when seeing the Eurogenes15 results for Kostenki14 was that it was contamination, but now seeing how they all lack that Caucasus / Near Eastern component makes me think it is the real deal. Why it's missing that area, and seeing how Kostenki14 is so close to there geographically though is intriguing.

A later creation maybe?

LeBrok
14-11-14, 04:39
Interesting comments. Here are the Eurogenes15, Dodecad12b, and DodecadV3 results for Ust' Ishim, Kostenki14 and Mal'ta:



Eurogenes15
Ust'-Ishim (http://www.y-str.org/2014/11/ust-ishim-ancient-dna.html)
Kostenki
14
Mal'ta

Dodecad K12b
Ust'-Ishim (http://www.y-str.org/2014/11/ust-ishim-ancient-dna.html)
Kostenki
14
Mal'ta

Dodecad V3
Ust'-Ishim (http://www.y-str.org/2014/11/ust-ishim-ancient-dna.html)
Kostenki
14
Mal'ta


North_Sea
-
18.81%
15.91%

Gedrosia
9.58%
12.38%
24.39%

East_European
4.55%
11.89%
20.03%


Atlantic
11.24%
12.39%
-

Siberian
2.70%
3.78%
13.55%

West_European
8.95%
30.62%
37.68%


Baltic
-
6.52%
6.54%

Northwest_African
2.58%
1.65%
-

Mediterranean
4.94%
15.55%
-


Eastern_Euro
3.08%
9.71%
38.02%

Southeast_Asian
13.76%
6.12%
-

Neo_African
3.76%
1.43%
0.38%


West_Med
4.82%
9.77%
-

Atlantic_Med
6.82%
21.46%
-

West_Asian
-
0.63%
-


West_Asian
-
-
-

North_European
7.39%
28.80%
47.46%

South_Asian
30.85%
17.75%
26.04%


East_Med
-
-
-

South_Asian
31.50%
15.70%
14.36%

Northeast_Asian
5.96%
4.58%
15.53%


Red_Sea
3.36%
5.70%
-

East_African
8.24%
3.87%
-

Southeast_Asian
21.76%
6.72%
-


South_Asian
30.76%
17.42%
20.31%

Southwest_Asian
3.36%
4.95%
-

East_African
7.03%
1.92%
-


Southeast_Asian
15.25%
1.33%
-

East_Asian
8.40%
0.15%
-

Southwest_Asian
3.86%
4.61%
-


Siberian
2.02%
0.66%
-

Caucasus
-
-
-

Northwest_African
3.25%
2.07%
-


Amerindian
2.20%
4.74%
18.62%

Sub_Saharan
5.67%
1.15%
0.24%

Palaeo_African
5.10%
2.24%
0.34%


Oceanian
10.96%
5.11%
0.12%












Northeast_African
10.08%
5.19%
-











Sub-Saharan
6.22%
2.66%
0.47%











None of them have the K12b Caucasus component, or the Eurogenes15 West_Asian or East_Med components, and Kostenki14 has just 0.63% of the West_Asian component in Dodecad V3.

My first thought when seeing the Eurogenes15 results for Kostenki14 was that it was contamination, but now seeing how they all lack that Caucasus / Near Eastern component makes me think it is the real deal. Why it's missing that area, and seeing how Kostenki14 is so close to there geographically though is intriguing.

Great observation dude. Whole region West Asia, East Med, and Caucasus is missing, or almost! Interestingly it is the place where agriculture started. We need genome of Near East hunter gatherer, probably very different than central and north Asians that we already have. Another idea is that farmers thanks to their big numbers mutated genome so fast that became incompatible for comparison with these old dudes.

Greying Wanderer
14-11-14, 04:45
@Angela

In that ANE post Martin Sikorra mentions Razib states the following:



http://www.unz.com/gnxp/ancestral-north-eurasians-about-the-world/

Why do Caucasians (The region, not the American term for whites) have such high Basal Eurasian component?

My thoughts on that so far are
1) they are largely descended from a mixed farmer/steppe population on the edge of the farmer/steppe zone who moved into the Caucasus as a refuge from PIE (so they get it from the farmer basal)
or
2) "basal" is a collection of 2+ similar signals and one of those signals originated in the Caucasus
or
3) a bit of both i.e. Caucasus has two basal signals, a farmer one and a local one.

Angela
14-11-14, 05:16
Lazaridis et al:

" We intersected the set of Near Eastern populations without substantial (<1%) African admixture asinferred by ADMIXTURE K=10 (SI 9) with those whose most significantf3-statistic involved the pairing (Stuttgart, MA1) (Table 1). Five populations met these criteria: Abkhasian, Chechen, Cypriot, Druze, Lezgin. We modified the model of Fig. S12.11 to model these populations as a mixture of a Near Eastern population that also contributed to Stuttgart and an MA1-related ANE population (but no WHG ancestry) (Fig. S12.19). All five populationsfit successfully, and we report their admixture proportions in Table S12.12.


Conversely, we do not currently know whether the signal of admixture observed in the Near East and Caucasus reflects an arrival of MA1-related ancestry from the east, or alternatively dilution of native MA1-related ancestry by an expansion of a Near Eastern population carrying Basal Eurasian admixture, associated perhaps with the expansion of Levantine Mesopotamian early agriculturalists who seem to have influenced the Y-chromosome distribution of the region19. Future studies of ancient Central Eurasians may help resolve such questions of migration timing and directionality."

Angela
14-11-14, 06:01
Aberdeen:I have some concerns that the way this paper is referring to basal Eurasians possibly involves a misunderstanding of what Lazardis et al meant when they referred to basal Eurasians as forming at least 44% of EEF. Based on what the word "basal" means, I can understand why there's an assumption in this paper that basal Eurasians are those Eurasians who existed before the split occurred in the out of Africa population in the Middle East. However, when I look at the paper on the three founding populations of Europe, it seems to refer to a population that split off from the original out of Africa group and evolved into something separate perhaps in Saudia Arabia and perhaps as a result of further gene flow from East Africa, so Lazardis's basal Eurasians who mixed with some other group (perhaps Balkan hunter gatherers) to become EEF were different from the original out of Africa group. Am I misunderstanding the issue? I don't see how the group that Lazardis considers to be Middle Eastern farmers who mixed with other populations as it flowed into Europe could have existed 36,000 years ago.:

This is the specific reference from Lazaridis et al. Basal Eurasian is " admixture from a source that branched off before the divergence of West Eurasians and eastern non-Africans.

The Near East was the staging point for the peopling of Eurasia by anatomically modern humans. As a result, it is entirely plausible that it harbored deep Eurasian ancestry which did not initially participate in the northward colonization of Europe, but was later brought into Europe by Near Eastern farmers. More speculatively, some basal Eurasian admixture in the Near East may reflect the early presence of anatomically modern humans7in the Levant, or the populations responsible for the appearance of the Nubian Complex in Arabia8, both of which date much earlier than the widespread dissemination of modern humans across Eurasia. Finally, it could reflect continuing more recent gene flows between the NearEast and nearby Africa after the initial out-of-Africa dispersal, perhaps associated with the spread of Y-chromosome haplogroup E subclades from eastern Africa9, 10 into the Near East, which appeared at least 7,000 years ago into Neolithic Europe11"

The problem for me with this formulation (and perhaps for you) is that the last possibility has nothing to do with a source which branched off before the divergence of West Eurasians and eastern non-Africans, and therefore it confuses the issue. As for his other speculations, I think he's talking about the theories having to do with an OOA event around 100, 000 years ago versus the more accepted, more recent OOA event. Perhaps it would have been better to stick with the more general theory that some AMH's stayed behind in the Near East when other groups went into Europe. Or perhaps it will turn out that Basal is a basically West Eurasian genome with a few percent African from the Red Sea. I don't know.

As to the study under discussion, I also have some doubts about whether the authors of this paper actually found Basal Eurasian in Kostenki 14. (I do think that the author has a point when he writes that they never said that Kostenki's descendants provided genetic material to Europeans. He's at pains to point out that a careful reading of their paper would have shown that in Model 2, they do not show Kostenki genes flowing into Europeans.)

I think, from Martin Sikorra's post, that they themselves have some doubts. What he says is that "K14 does share substantial amount of ancestry with Mesolithic Hunter-gatherers (and therefore modern Europeans by extension), but at the same time appears less close to East Asians than all Western Eurasians...Therefore if you take the Lazaridis et al. model as a backbone, you need some extra gene flow to account for that, be it from Basal Eurasian into K14, or some sort of basal gene flow between East Asia and early West Eurasians, post-K14 but pre-ANE/HG split. While we don’t have the resolution to be sure, our results do suggest that K14 was close to or a already somewhat down the HG branch of the ANE/HG split, which implies that those proposed components would not only have to be already somewhat differentiated by 36 kya, but also already have had mixed to a certain extent".

Dienekes in his commentary also implied, I think, that there is some data that could call this finding into question.

At any rate, even if Kostenki 14 contained some input from Basal Eurasians, I don't know that it poses a big problem for the Lazardis model. It's clear there was no Basal Eurasian in the WHG or the people of central Europe, at least, until after the Neolithic. As for where Kostenki 14 might have picked up his "Basal", if he has it, I think all he (his people) would have had to have done is graze the area where the Basal Eurasian lived, which wouldn't necessarily have had to have been limited to Arabia, especially by this point.

Ed. I think we also have to be prepared for the fact that, as they kept saying in the Lazaridis paper, this model was based on the ancient genomes they had at the time. As more samples are recovered, especially from the Near East, some of the models may indeed change. I don't think, however, that refining the nature of the "Basal Eurasian" component or figuring out the best model for ancient admixtures on one or another side of some apparently very important east/west line is going to change the utility of the Lazardis model for the peopling of Europe. We have a genome for an early European farmer, who is very similar to other European farmers. We have the genomes of western hunter gatherers who were in Europe before the arrival of the Europeans, and we have the genome of a North Eurasian whose genes made a late appearance. Through them, we can learn about the peopling of Europe and about the relationships between the different European ethnicities. I don't think that will change.

Greying Wanderer
14-11-14, 08:19
"Through them, we can learn about the peopling of Europe and about the relationships between the different European ethnicities. I don't think that will change."

I think teasing out the basal(s) may provide clues to the earliest layers e.g. ASE/ASI etc, and their sequence across Eurasia as a whole.

Alan
14-11-14, 09:37
Btw regrading your subsequent ANE post, I can confirm that those are the Kalash. Interesting also that the correspondingly the Kalash ADMIXTURE component shows up in MA1, but is almost absent in K14 (see our Figure S20).


What does that mean? Are Kalash the best proxy for ANE?

epoch
14-11-14, 10:20
to EPOCH
the link with Y-N is not evident - these regions were run also by Y-C (the supposed SNP of this man) and later by Y-R* bearers too -
keep in mind Y-N1 is not so old in Finland Estonia (Bronze Age?)

Ust-Ishim Y-DNA supposedly could have been ancestral to NO, if I understand all well. Perhaps I posted this map in the wrong thread. Sorry for that.

Angela
14-11-14, 19:09
I suppose I should have posted Razib Khan's original piece on the Willerslev, Sikorra paper on Kostenki 14 before I posted Martin Sikorra's rebuttal. Here is the link:
http://www.unz.com/gnxp/a-man-30000-years-before-his-time/

It's 2600 words,but there's a lot in it to chew over...

(I know I shouldn't editorialize, but I can't help but comment that the rather silly, in my opinion, comments by Willerslev don't do his paper any good. I'm doubtful about some of the paper's analyses. I'm not at all doubtful that his conclusions, as reported from his interview in Science, are most probably wrong.)

Aberdeen
14-11-14, 19:44
This is the specific reference from Lazaridis et al. Basal Eurasian is " admixture from a source that branched off before the divergence of West Eurasians and eastern non-Africans.

The Near East was the staging point for the peopling of Eurasia by anatomically modern humans. As a result, it is entirely plausible that it harbored deep Eurasian ancestry which did not initially participate in the northward colonization of Europe, but was later brought into Europe by Near Eastern farmers. More speculatively, some basal Eurasian admixture in the Near East may reflect the early presence of anatomically modern humans7in the Levant, or the populations responsible for the appearance of the Nubian Complex in Arabia8, both of which date much earlier than the widespread dissemination of modern humans across Eurasia. Finally, it could reflect continuing more recent gene flows between the NearEast and nearby Africa after the initial out-of-Africa dispersal, perhaps associated with the spread of Y-chromosome haplogroup E subclades from eastern Africa9, 10 into the Near East, which appeared at least 7,000 years ago into Neolithic Europe11"

The problem for me with this formulation (and perhaps for you) is that the last possibility has nothing to do with a source which branched off before the divergence of West Eurasians and eastern non-Africans, and therefore it confuses the issue. As for his other speculations, I think he's talking about the theories having to do with an OOA event around 100, 000 years ago versus the more accepted, more recent OOA event. Perhaps it would have been better to stick with the more general theory that some AMH's stayed behind in the Near East when other groups went into Europe. Or perhaps it will turn out that Basal is a basically West Eurasian genome with a few percent African from the Red Sea. I don't know.

As to the study under discussion, I also have some doubts about whether the authors of this paper actually found Basal Eurasian in Kostenki 14. (I do think that the author has a point when he writes that they never said that Kostenki's descendants provided genetic material to Europeans. He's at pains to point out that a careful reading of their paper would have shown that in Model 2, they do not show Kostenki genes flowing into Europeans.)

I think, from Martin Sikorra's post, that they themselves have some doubts. What he says is that "K14 does share substantial amount of ancestry with Mesolithic Hunter-gatherers (and therefore modern Europeans by extension), but at the same time appears less close to East Asians than all Western Eurasians...Therefore if you take the Lazaridis et al. model as a backbone, you need some extra gene flow to account for that, be it from Basal Eurasian into K14, or some sort of basal gene flow between East Asia and early West Eurasians, post-K14 but pre-ANE/HG split. While we don’t have the resolution to be sure, our results do suggest that K14 was close to or a already somewhat down the HG branch of the ANE/HG split, which implies that those proposed components would not only have to be already somewhat differentiated by 36 kya, but also already have had mixed to a certain extent".

Dienekes in his commentary also implied, I think, that there is some data that could call this finding into question.

At any rate, even if Kostenki 14 contained some input from Basal Eurasians, I don't know that it poses a big problem for the Lazardis model. It's clear there was no Basal Eurasian in the WHG or the people of central Europe, at least, until after the Neolithic. As for where Kostenki 14 might have picked up his "Basal", if he has it, I think all he (his people) would have had to have done is graze the area where the Basal Eurasian lived, which wouldn't necessarily have had to have been limited to Arabia, especially by this point.

Ed. I think we also have to be prepared for the fact that, as they kept saying in the Lazaridis paper, this model was based on the ancient genomes they had at the time. As more samples are recovered, especially from the Near East, some of the models may indeed change. I don't think, however, that refining the nature of the "Basal Eurasian" component or figuring out the best model for ancient admixtures on one or another side of some apparently very important east/west line is going to change the utility of the Lazardis model for the peopling of Europe. We have a genome for an early European farmer, who is very similar to other European farmers. We have the genomes of western hunter gatherers who were in Europe before the arrival of the Europeans, and we have the genome of a North Eurasian whose genes made a late appearance. Through them, we can learn about the peopling of Europe and about the relationships between the different European ethnicities. I don't think that will change.

I'm not disagreeing with the Lazardis model for the peopling of Europe. I'm just pointing out that the Middle Eastern early farmers who mixed with some other group (possibly Balkan hunter gatherers) to produce EEF must have evolved away somewhat from any group of basal Eurasians that contributed to the genes of Kostenki 14, as a result of other gene flow and/or genetic drift during the intervening thousands of years between Kostenki 14 and the first Middle Eastern farmers. So perhaps Lazardis should have called his group something else, such as "derived from basal Eurasians".

epoch
14-11-14, 22:50
Davidski at eurogenes is mentioning:

http://eurogenes.blogspot.nl/2014/11/treemix-graphs-with-kostenki14-and-ust.html


I'm quite certain now that the so called Basal Eurasian ancestry carried by Stuttgart and Kostenki14 can't be lumped into a single component.

Ok. Then what part of the mediterranean admixture (eef/basal) is from Kostenski14 and what from EEF? K14 keeps scoring low on Middle-East. Genetiker has a page up too, and there you see the same low Near-Eastern scores. Also, check the phenotype list there.

http://genetiker.wordpress.com/2014/11/14/analyses-of-the-kostenki-14-genome/

Alan
15-11-14, 14:02
Interesting comments. Here are the Eurogenes15, Dodecad12b, and DodecadV3 results for Ust' Ishim, Kostenki14 and Mal'ta:



Eurogenes15
Ust'-Ishim (http://www.y-str.org/2014/11/ust-ishim-ancient-dna.html)
Kostenki
14
Mal'ta

Dodecad K12b
Ust'-Ishim (http://www.y-str.org/2014/11/ust-ishim-ancient-dna.html)
Kostenki
14
Mal'ta

Dodecad V3
Ust'-Ishim (http://www.y-str.org/2014/11/ust-ishim-ancient-dna.html)
Kostenki
14
Mal'ta


North_Sea
-
18.81%
15.91%

Gedrosia
9.58%
12.38%
24.39%

East_European
4.55%
11.89%
20.03%


Atlantic
11.24%
12.39%
-

Siberian
2.70%
3.78%
13.55%

West_European
8.95%
30.62%
37.68%


Baltic
-
6.52%
6.54%

Northwest_African
2.58%
1.65%
-

Mediterranean
4.94%
15.55%
-


Eastern_Euro
3.08%
9.71%
38.02%

Southeast_Asian
13.76%
6.12%
-

Neo_African
3.76%
1.43%
0.38%


West_Med
4.82%
9.77%
-

Atlantic_Med
6.82%
21.46%
-

West_Asian
-
0.63%
-


West_Asian
-
-
-

North_European
7.39%
28.80%
47.46%

South_Asian
30.85%
17.75%
26.04%


East_Med
-
-
-

South_Asian
31.50%
15.70%
14.36%

Northeast_Asian
5.96%
4.58%
15.53%


Red_Sea
3.36%
5.70%
-

East_African
8.24%
3.87%
-

Southeast_Asian
21.76%
6.72%
-


South_Asian
30.76%
17.42%
20.31%

Southwest_Asian
3.36%
4.95%
-

East_African
7.03%
1.92%
-


Southeast_Asian
15.25%
1.33%
-

East_Asian
8.40%
0.15%
-

Southwest_Asian
3.86%
4.61%
-


Siberian
2.02%
0.66%
-

Caucasus
-
-
-

Northwest_African
3.25%
2.07%
-


Amerindian
2.20%
4.74%
18.62%

Sub_Saharan
5.67%
1.15%
0.24%

Palaeo_African
5.10%
2.24%
0.34%


Oceanian
10.96%
5.11%
0.12%












Northeast_African
10.08%
5.19%
-











Sub-Saharan
6.22%
2.66%
0.47%











None of them have the K12b Caucasus component, or the Eurogenes15 West_Asian or East_Med components, and Kostenki14 has just 0.63% of the West_Asian component in Dodecad V3.

My first thought when seeing the Eurogenes15 results for Kostenki14 was that it was contamination, but now seeing how they all lack that Caucasus / Near Eastern component makes me think it is the real deal. Why it's missing that area, and seeing how Kostenki14 is so close to there geographically though is intriguing.


The explanatio n is simple, "Gedrosia" is more of the "West Asian" component than "Caucasus" is.

http://1.bp.blogspot.com/-v80ztSRUM9E/UE3JklSVh5I/AAAAAAAAGUg/cUR5Ps2TBA8/s1600/_7.png


Gedrosia is 90% "West Asian" of K7b + 10% "ANI".

Caucasus is ~55% "West Asian", *37% "Southern" and ~8% Atlantic_Baltic. This is why Ötzi showed in some calculators NO West Asian but in K12b some "Caucasus". It is the "Southern" portion inside Caucasus which shows up and not the West Asian portion but for some kind of reason people seem to never understand that. The West Asian portion of Mal'ta is much more of the Gedrosia type, which makes quite sense since Gedrosia is the "purer" portion of "West Asian" and which is much more widespred in South_Central and East Asia compared to Caucasus.

Also as I wrote earlier. In Eurogenes 15 and Dodecad v3 the West Asian (Gedrosia) gets eaten up by South Asian and some of the other West Asian portions get eaten up by various "North European" components.

We know that from the Lazaridis paper where North Caucasians who score high in ANE are shown with almost 40% (North)"European" ( Most Caucasians have 20-26% North European the rest must be Caucasus which has been labeled under European) and substantial South Asian (which they in reality lack and can be only explained with that Gedrosia has been put under the South Asian label).

Davidski made it's own run with a differen't calculator on Mal'ta genome. And he came to the conclusion that the sample can be explained as 30% North European like, 25% Caucasus_Gedrosia(more Gedrosia than Caucasus) like, 25% Amerindian like and the rest was ASI and Southeast Asian like.

Angela
15-11-14, 16:24
I'm not disagreeing with the Lazardis model for the peopling of Europe. I'm just pointing out that the Middle Eastern early farmers who mixed with some other group (possibly Balkan hunter gatherers) to produce EEF must have evolved away somewhat from any group of basal Eurasians that contributed to the genes of Kostenki 14, as a result of other gene flow and/or genetic drift during the intervening thousands of years between Kostenki 14 and the first Middle Eastern farmers. So perhaps Lazardis should have called his group something else, such as "derived from basal Eurasians".

Or, the Willerslev Lab paper is just wrong in parts of its analysis and has confused the issue. The more that the paper sort of percolates away on a back burner in my brain, the less confident I am of some of those conclusions.

I think further resolution is going to have to wait until we have more ancient samples, particularly from the ancient Near East, and hopefully from South Asia, but just generally we may indeed be looking at a situation where there was a first split after OOA (the Lazaridis "Basal Eurasian"), and then subsequent differentiation of the remaining lineage. What Willerslev and company are calling "basal" in K14 might just reflect ancestry further up the tree from La Brana, Loschbour, Motala and even ANE, ancestry which is more similar to the "Basal" in Stuttgart and therefore in the Ancient Near Eastern farmers from whom EEF received it.

As for the "African" affinity in the Lazaridis "Basal Eurasian", I think it partly stems from the fact that as the first split in the tree it's bound to have more similarities to that original lineage even if there was a lot of subsequent drift. (The other lineage(s) are, of course, experiencing their own drift.)

Adding to that is the fact that increasingly it looks to me as if the speculation that Y dna "E" formed in West Asia and then back migrated to Africa might be correct. Even in the Yoruba, there are traces of what has been called "West Eurasian" but may be "Basal" Eurasian. That's not to say that over thousands of years some additional "African" might not have seeped north into the Near East and then onward, just as some "African" seeped north, I think, through North Africa, up through Iberia, especially the western portion, and then through the whole western facade of Europe, although by that point the signal would have been much weaker. That's why IBD analysis shows the most SSA in Iberia, (followed, in Europe, by Sicily etc.) The East Africans are also an example of the back and forth migrations from West Asia and Africa, the most recent of which has to do with the Arab slave trade.

To me, it thus does indeed look as if there were a lot of migrations and admixtures throughout human history, ( look at South Asia, for example) which is why I so disagree with Willerslev's comments in Science about people just basically staying put and breeding at the edges. Has he looked at the journey that the y lineages alone have made?)

I do agree that the names for some of these more ancient components probably need to be re-worked once the relationships are clearer.

Angela
15-11-14, 20:10
http://genetiker.wordpress.com/2014/11/14/analyses-of-the-kostenki-14-genome/[/URL]

Very confusing. I've only gone through the Willerslev Lab paper once, but I didn't see anything about phenotype. Did they feel the coverage was too spotty to make pronouncements?

On the other hand, in reporting there is this in the Science interview with Willerslev:

See:
http://news.sciencemag.org/archaeology/2014/11/european-genetic-identity-may-stretch-back-36000-years

"From the sequence data, they found gene variants indicating that the man had dark skin and eyes."

LeBrok
15-11-14, 22:10
Very confusing. I've only gone through the Willerslev Lab paper once, but I didn't see anything about phenotype. Did they feel the coverage was too spotty to make pronouncements?

On the other hand, in reporting there is this in the Science interview with Willerslev:

See:
http://news.sciencemag.org/archaeology/2014/11/european-genetic-identity-may-stretch-back-36000-years

"From the sequence data, they found gene variants indicating that the man had dark skin and eyes."
I wonder if Prairie Indians or any Northern Natives, DNA was sequenced in America, and what color of skin we can infer from their DNA? They are not dark skinned, although a bit darker than most Europeans.
Their hunter gatherer origin would imply dark or medium brown skin colour, if our knowledge of skin color alleles is fairly good. I'm sure they don't have much of farmer DNA in them, and some tribes met first white man 100 years ago. Not enough time to distribute skin color genes through entire communities.

JS Bach
15-11-14, 22:47
I wonder if Prairie Indians or any Northern Natives, DNA was sequenced in America, and what color of skin we can infer from their DNA? They are not dark skinned, although a bit darker than most Europeans.
Their hunter gatherer origin would imply dark or medium brown skin colour, if our knowledge of skin color alleles is fairly good. I'm sure they don't have much of farmer DNA in them, and some tribes met first white man 100 years ago. Not enough time to distribute skin color genes through entire communities.

Some food for thought -- According to Genetiker, both Afontova Gora 2 and Motala 12 (19% ANE) had both copies of the derived allele for rs1426654:

"Mal’ta 1 had two copies of the ancestral allele of rs1426654, but Afontova Gora 2 had two copies of the derived allele. This SNP is located in the gene SLC24A5, and its derived allele is one of the two major Caucasoid depigmentation mutations. The other major Caucasoid depigmentation mutation is the derived allele of rs16891982, in the gene SLC45A2.

So we now know that Stora Förvar 11, who lived 7,500 years ago in Sweden, had the SLC45A2 mutation, and that Motala 12, who lived 8,000 years ago in Sweden, and Afontova Gora 2, who lived 17,000 years ago in Siberia, had the SLC24A5 mutation."

http://genetiker.wordpress.com/2014/05/28/pigmentation-snp-genotypes-for-malta-1-and-afontova-gora-2/

Here's where he says Motala 12 had both copies of the derived allele of rs1426654: http://genetiker.wordpress.com/2014/10/02/pigmentation-snp-genotypes-for-motala-hunter-gatherers/

epoch
16-11-14, 09:09
The derived allels for K14's phenotype are:



ASIP rs2424984 TC Veddoid brown skin
MC1R rs1805007 TC red hair, fair skin
OCA2 rs1800414 CC Mongoloid light skin
TYR rs1393350 GA blond hair, blue eyes


No KITLG, TYRP or any of the more modern variations. Also, he appears to have had:



MCM6 rs182549 CT ability to digest milk


Found on the page of Genetiker.

Furthermore, in the reaction thingy of eurogenes Srkz has put up an IBD map of K14:

http://eurogenes.blogspot.nl/2014/11/treemix-graphs-with-kostenki14-and-ust.html?showComment=1416037667868#c69214585477700 22451

http://s013.radikal.ru/i325/1411/80/9c75759aae62.png

ElHorsto
16-11-14, 16:28
The derived allels for K14's phenotype are:



ASIP rs2424984 TC Veddoid brown skin
MC1R rs1805007 TC red hair, fair skin
OCA2 rs1800414 CC Mongoloid light skin
TYR rs1393350 GA blond hair, blue eyes


No KITLG, TYRP or any of the more modern variations. Also, he appears to have had:



MCM6 rs182549 CT ability to digest milk


Found on the page of Genetiker.

Furthermore, in the reaction thingy of eurogenes Srkz has put up an IBD map of K14:

http://eurogenes.blogspot.nl/2014/11/treemix-graphs-with-kostenki14-and-ust.html?showComment=1416037667868#c69214585477700 22451

http://s013.radikal.ru/i325/1411/80/9c75759aae62.png

So whole Europe is close to maximally red, except Basques, Sardinians, Ashkenazi (not so strong), Erzya and Udmurts. Some slight weakness seems to be also in Saami, Karelians, Estonian and Veps. Probably Finns would also show some slight weakness. All these folks are non-IE speakers. Else only Yugoslavs show a very slight weakness if I can see it right.
Bashkiria (R1b land) is max. red, same for Balts and eastern Slavs (R1a land).
And then there is that trail down to north India.

Angela
16-11-14, 19:33
So whole Europe is close to maximally red, except Basques, Sardinians, Ashkenazi (not so strong), Erzya and Udmurts. Some slight weakness seems to be also in Saami, Karelians, Estonian and Veps. Probably Finns would also show some slight weakness. All these folks are non-IE speakers. Else only Yugoslavs show a very slight weakness if I can see it right.
Bashkiria (R1b land) is max. red, same for Balts and eastern Slavs (R1a land).
And then there is that trail down to north India.

I also thought that perhaps it was carried by the Indo-Europeans, but while I see what you mean where the Basques are concerned, I thought Sardinia looked pretty "red". Of course, especially in recent years, there's been a lot of input from the mainland. You don't have the language difference as a barrier the way you do with the Basques.

ElHorsto
16-11-14, 20:04
I also thought that perhaps it was carried by the Indo-Europeans, but while I see what you mean where the Basques are concerned, I thought Sardinia looked pretty "red". Of course, especially in recent years, there's been a lot of input from the mainland. You don't have the language difference as a barrier the way you do with the Basques.

Not quite. Sardinia is brown compared to Italy. (click to enlarge)
6853

Also it's probable that Spaniards as neighbours of Basques also have a bit less red color, but I'm not sure.

MOESAN
16-11-14, 22:37
[QUOTE=bicicleur;443760]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[/QUOTE

assumption - how can you say they are extinct lines?: it could be the case, but a lot of autosomals common to them have surely been passed to further generations by their brethren, or I mistake? the majority of autosomals -biallelic- don't undergo the same destiny and rapid drift as Y-haplogroups - some genes disappear (mutate) but not all of them - it's not always the same genes which are transmitted to individual descendants but as a whole the populational origin assumed to these passed genes is not erased so quickly ? (sorry for the my limited english)

Angela
16-11-14, 23:08
El Horsto: Not quite. Sardinia is brown compared to Italy. (click to enlarge)
http://www.eupedia.com/forum/attachment.php?attachmentid=6853&d=1416161063&thumb=1 (http://www.eupedia.com/forum/attachment.php?attachmentid=6853&d=1416161063)



Yes, with better resolution, you're right.

It's a little off in terms of strict correlation with ANE, perhaps because it's a combination signal with both WHG and ANE, and a little of other things as well? ANE for Sardinians is 8%, for Basques it's .114, which is actually a little more than for north Italy, which is .108.

Look at this old Cavalli-Sforza map based only on blood proteins:
http://www.bmanuel.org/corling/euIt_comp3++_.jpg (http://www.bmanuel.org/corling/eur_comp3++_.jpg)

Unfortunately, Sardinia isn't included.

Angela
16-11-14, 23:21
MOESAN:
assumption - how can you say they are extinct lines?: it could be the case, but a lot of autosomals common to them have surely been passed to further generations by their brethren, or I mistake? the majority of autosomals -biallelic- don't undergo the same destiny and rapid drift as Y-haplogroups - some genes disappear (mutate) but not all of them - it's not always the same genes which are transmitted to individual descendants but as a whole the populational origin assumed to these passed genes is not erased so quickly ? (sorry for the my limited english)

I agree. Loschbour and Stuttgart may be 8.000 years old, but our genomes can be compared to theirs, and we can know how much of them is in us.

That said, when we're talking about an ancient genome 36,000 years old, and there has been so much admixture and combinations since then, I think all we can get is hints about possible influences. I'm amazed that figuring out the "tree" at such time depth so engages so many amateurs.

Greying Wanderer
18-11-14, 00:52
I agree. Loschbour and Stuttgart may be 8.000 years old, but our genomes can be compared to theirs, and we can know how much of them is in us.

That said, when we're talking about an ancient genome 36,000 years old, and there has been so much admixture and combinations since then, I think all we can get is hints about possible influences. I'm amazed that figuring out the "tree" at such time depth so engages so many amateurs.


I don't know. I think figuring out the very ancient patterns with dna might turn out to be easier than figuring out the modern pattern because as you say there will be fewer layers - although I expect it will be easier when there are enough ancient samples to compare with each other rather than trying to work backwards from more modern populations with more layers. In the interim though using modern populations to try and tease out clues is fun imo.

MOESAN
22-11-14, 13:16
Looking at some ancient genomes through Eurogenes15, it'sstriking how Mal'ta lacks the Atlantic component that Ust'-Ishim has:

Seeingas Mal'ta was Y-dna R, this leads me away from thinking the Atlanticcomponent is associated with R. Although I understand how weakcorrelations between uni-parental and autosomal markers are thesedays, maybe in ancient times those associations werestronger.

surprisesoccur more than a time:
1- some links between today well separatedpopulations can be due to ancient continuum disrupted by a morerecent colonisation-
2- even if a kind of continuum existed it canbreak down by time and geography distances and if a big enough stockof common genes existed before some discrepancies can occurconsidering the human populations were very scarce in old time -
3-a very more recent colonisation can have brought some % of genes of aremote population (see the 'gedrosia' question in NorthwestEurope)
that said, globally, Ust-Ishim is MORE SOUTHERN thanMalta, MORE ANCIENT, and the genes present among Atlantic people canbe linked to their ANCIENT MEDITERRANEAN statute more than to theireven MORE ANCIENT Hunter Gatherer COMPONANT evenif there is cohabitation of the two sources...- I'msure already evolved 'mediterraneans' occuped South and WesternEurope BEFORE Neolithic (see the second Mesolithic of some studiesjust preceding and pushed by Neolithic advance in mediterraneancoastal areas before climbing towards Northwest Europe ; it'sonly one of the possible introgressions of southern people in westernEurope ; but people of Muge Portugal (mesolithic) already shewsoutheastern accretions in morphology I cannot see as in situevolution) -



somenaive speculations for the fun :
'gedrosia'is one of the good questions : U-I, K14 and M'ta have a good bitof it when they present NO 'caucasus' at all in the same Dod-K12B andno 'west-asian' in other run, that said, it's the younger M'ta whohas the more spite its geographic eastern position, when the olderU-I has the lesser – so 'gedrosia could be a former element (if notall) in 'west-asian' or 'caucasus' but born by some previouspool come from where? - at first sight it gained weight by timeand was the heavier among the lattest population, M'ta, situated inCentral-Eastern Asia (Siberia) – the more sensible would be,believe, that the 'gedrosia' componant taking size underwent a lot ofmutations after the 22000 BC giving birth to the 'caucasus' and themutated part of 'west-asian' ? In some way 'gedrosia' doesn'tseem the direct recent heir of a 'southernwhite' componant and seemshaving grown in a northeastern enough region compared to today'caucasian' or « white » populations... so a « steppic »componant ?!? its today distribution among principallyindo-european speaking todayor past populations(I think here to the turkicized ones as the Turkmen) of western Asiais maybe not a hazard ? (look at Celts and Northern-Germanics) –and it could be that the pooled 'westasian' component would be a mixof 'southernwhite' and 'gedrosia' more or less mutated ? Thatsaid as a whole the 'southasian' seems ancient enough and could havegiven birth to 'gedrosia' with a drift more northern ??? - heresomething very speculative : an ancient 'south-asian' (not thetoday specialized one) pool gave birth to 'gedrosia' which climbednorthwards and later was pushed southwards giving birth to caucasusvariant of 'westasian not without some mix with 'southwest-asian'???



linkedquestions : no 'east-med' in any of the 3, but more'northeast-africa' and more 'east-africa' among the older U-I ANDalso a bit 'mediter' among U-I (but after K14) and/or always afterK14, a bit 'red-sea' or 'southwest-asian' among U-I ; shorltysaid, M-ta doesn't show any of the 'white-southern' or'red-sea-mediterranean-junction' pools, when otherwise the order isalways K14 before U-I... - could I say the 'east-med' is one of theevolutions of 'red-sea' (linked to 'northeast-africa'?)
'atlantic'et 'atlantic-med' : same order : K14 >> U-I, and 0%for M'ta = here the 'atlantic' has the same tendancies as othersouthern poolings -
sothe older men had southern components but little northern ones – 2hypothesis : a) the northern componants, present at Mesolithicin Europe, are derived from older 'southernlike' components OR b)they existed more easternly (came from N-India ???) based onother basic component and increased between 43000 and 36000 beforegoing more westwards -
:couldbe linked more to an ancient basic composition of 'westasian'('gedrosia' is present only among ANE and ANE is very North-Northeastdrifted) ...
I think we are all related, and that more recenttypes matured lately by different mutations + selections of geneswith a previous vaste from near-eastern to East-India (?) and twosecondary centers : Caucasus-Near-Eastern and Eastern Eurasia -the tendancy is to fragment at first as populations grow up andsedentarize - the first layer of men, spred on a larger scale, wasmaybe centered closer to North-India, but covered lands from Siberiato Western Europe before new hearths appeared?
what I say issummarized by the fact Ust-Ishim spans more today population and hadlinks with Oceanians (very primitivelike and apparently born by afirst wave out of Africa without staying too long time inNear-Eastern-Arabia) but also to Africans and East Asians -
heis surely not theresult of crossings of already as evolved populations as our modernones ! -
bythe way, Mal'ta is the younger in the team and it's not so surprisingto find in it Y-R which is a well evolved and severely mutated groupof ligneages – plus : the 'asian' components it shows areaccording to less-to-more detailed poolings : 'northasian', or'siberian', or 'amerindian' this last one canbe a a late enoughevolution in situ or a return from America ??? (only precisestudies can answer that, what is outside my present play)
inprovisary conclusion of this profane 's exercice of mine withouttraced ligneages of genes nor « distances » calculation :some components apparently recently present could be the evolution inan human group or the result of an admixture with a foreign group...



somesupra-populations groupings by myself (only partly reliable):
southwestern-whites :
Euro15 :K : 18,09 // U-I : 14,60 // M'ta : 0,00
DodK12b :K : 26,41 // U-I : 10,18 // M'ta : 0,00
Dod-V13 :K : 20,16 // U-I : 8,80 // M'ta:0,00
southasian :
Euro15 :U-I : 30,76 // M'ta : 20,31 // K :17,42
DodK12b :U-I : 31,50 // K : 15,70 // M'ta : 14,36 !!!
Dod-V13 :U-I : 30,85 // M'ta: 26,04 // K : 17,75
+
gedrosia :
DodK12b :M'ta : 24,39 // K : 12,38 // U-I : 9,58
+
centersouthasian :
DodK12b :M'ta : 50,43 / U-I : 40,43 // K : 30,13



north-northeasteuropean :
Euro15 :M'ta : 60, 47 // K : 35,04 // U-I : 3,08
DodK12b :M'ta : 47,46 // K : 28,80 // U-I : 7,39
Dod-V3 :M'ta : 37,68 // K : 30,62 // U-I : 8,95

JS Bach
12-12-14, 06:12
There's a new Eurogenes youtube channel that has a video depicting the Eurogenes15 breakdown of a dozen-or-so ancient European genomes, as well as breakdowns of some modern population groups here: https://www.youtube.com/watch?v=n58rgWVUups The only component that shows up in all of the genomes is the Atlantic component. The first two genomes they present are the Hunter-Gatherers: Motala12 and Loschbour (both about 7,500 ybp.) Motala12 has about 10% Atlantic, and Loschbour has a little under 30% Atlantic. They both also have high percentages of the North Sea and Baltic components. In contrast, the farmers clearly do tend to have more of the Atlantic component, compared with the North Sea, Baltic, and East Euro components. So certainly the Atlantic component is associated with the Neolithic farmers, but it's also associated with the Hunter-Gatherers as well, as Motala12 and Loschbour indicate. I wonder what more ancient Western European genomes will show in the future?

Alan
13-12-14, 05:36
Look what I found

https://dnaexplained.files.wordpress.com/2014/10/hammer-2014-32.jpg


So basically as I thought. The best genetic proxy for Ancient North Eurasians were the Kalash.

JS Bach
13-12-14, 06:47
I like that graph. Notice how the ANE component is yellow. I wonder if it was the component that brought the blond hair. The south-western European countries with low ANE don't have high blond hair rates. It's interesting how the ANE proportions are relatively uniform among the rest of the European countries there. Some of the Kalash have blond hair - just google it. It would be nice to have the results for Afontova Gora 2 there too. Also, the Mal'ta boy's genes suggest he would have had brown hair (I guess rather than black): http://www.nytimes.com/2013/11/21/science/two-surprises-in-dna-of-boy-found-buried-in-siberia.html?pagewanted=all&_r=0 Maybe blond hair came about with ANE in Siberia there.

LeBrok
13-12-14, 07:08
I don't really buy it. Till we get a genome of real NEF we should get carried away with this. They could be related to WHG somewhat and this would make NEF genom proportion bigger in Europeans.
What is with the naming anyway? "Asian Steppe Invaders"? They didn't invade the steppe. They were from the steppe.

Alan
13-12-14, 07:14
I like that graph. Notice how the ANE component is yellow. I wonder if it was the component that brought the blond hair. The south-western European countries with low ANE don't have high blond hair rates. It's interesting how the ANE proportions are relatively uniform among the rest of the European countries there. Some of the Kalash have blond hair - just google it. It would be nice to have the results for Afontova Gora 2 there too. Also, the Mal'ta boy's genes suggest he would have had brown hair (I guess rather than black): http://www.nytimes.com/2013/11/21/science/two-surprises-in-dna-of-boy-found-buried-in-siberia.html?pagewanted=all&_r=0 Maybe blond hair came about with ANE in Siberia there.

Unlikely that ANE brought Blond Hair, because the very first European to have the combination of light eyes, skin and hair was a farmer from Hungary. I don't think that these traits collerate with some ancient components. It's more of an "Caucasian" thing. And could have evolved in groups with various backgrounds.

JS Bach
13-12-14, 07:39
Unlikely that ANE brought Blond Hair, because the very first European to have the combination of light eyes, skin and hair was a farmer from Hungary.

Good point. I assume you mean NE7. He doesn't appear to have any ANE.

Greying Wanderer
13-12-14, 07:53
I don't really buy it. Till we get a genome of real NEF we should get carried away with this. They could be related to WHG somewhat and this would make NEF genom proportion bigger in Europeans.
What is with the naming anyway? "Asian Steppe Invaders"? They didn't invade the steppe. They were from the steppe.

Look at the font.

Greying Wanderer
13-12-14, 07:58
Unlikely that ANE brought Blond Hair, because the very first European to have the combination of light eyes, skin and hair was a farmer from Hungary. I don't think that these traits collerate with some ancient components. It's more of an "Caucasian" thing. And could have evolved in groups with various backgrounds.

I think blond hair is likely the product of mixture of different depigmentation genes that occurred among different populations - possibly for different reasons. For example say it takes three components and some populations only have two. ANE could have brought one of the components.

LeBrok
13-12-14, 10:05
Look at the font. ?
I need some help with this.

Aberdeen
13-12-14, 15:04
Look what I found

https://dnaexplained.files.wordpress.com/2014/10/hammer-2014-32.jpg


So basically as I thought. The best genetic proxy for Ancient North Eurasians were the Kalash.

Something is off here. I thought MA-1=ANE but if you look near the top, MA-1 has only partial ANE, less than Kalash. And what is Asian Steppe Invader?

Greying Wanderer
13-12-14, 18:45
?
I need some help with this.

It's photo shopped. Look at the font of "Asian Steppe Invader". The angle/light is wrong.


"EEF" "WHG" "ANE" and "MA1" look a bit off too but it's not so clear.

LeBrok
13-12-14, 19:52
It's photo shopped. Look at the font of "Asian Steppe Invader". The angle/light is wrong.


"EEF" "WHG" "ANE" and "MA1" look a bit off too but it's not so clear.

I see it now, you could be right. The first picture was taken from computer screen and then "Steppe Invader" added during editing of this new picture.

JS Bach
13-12-14, 22:37
I think blond hair is likely the product of mixture of different depigmentation genes that occurred among different populations - possibly for different reasons. For example say it takes three components and some populations only have two. ANE could have brought one of the components.

That reminds me, Genetiker made a post where he computed the frequencies of the SNP most strongly associated with blue eyes for many different populations here: https://genetiker.wordpress.com/2013/06/01/frequencies-for-blue-eyes-snp-rs12913832-in-hgdp-populations/

And apparently, for the Karitiana (an isolated south American tribe) 34.6% of them have at least one G, and 7.7% of them have both G's. And the G allele is present in lower frequencies in some other Amerindian tribes.

I wouldn't have thought that something like 7.7% of the Karitiana would have blue (or green) eyes - at least, I've never heard of any of them with that trait - although I could be wrong. Maybe there are other genes that Europeans have that influence having blue eyes, that are lacking in the Karitiana.

LeBrok
13-12-14, 23:04
That reminds me, Genetiker made a post where he computed the frequencies of the SNP most strongly associated with blue eyes for many different populations here: https://genetiker.wordpress.com/2013/06/01/frequencies-for-blue-eyes-snp-rs12913832-in-hgdp-populations/

And apparently, for the Karitiana (an isolated south American tribe) 34.6% of them have at least one G, and 7.7% of them have both G's. And the G allele is present in lower frequencies in some other Amerindian tribes.

I wouldn't have thought that something like 7.7% of the Karitiana would have blue (or green) eyes - at least, I've never heard of any of them with that trait - although I could be wrong. Maybe there are other genes that Europeans have that influence having blue eyes, that are lacking in the Karitiana.
True, genetic research into depigmentation is not complete yet.

Alan
14-12-14, 00:03
?
I need some help with this.

Edit: I see you guys are right the "Asian Steppe Invaders" was probably edited into it.

Alan
14-12-14, 00:05
Something is off here. I thought MA-1=ANE but if you look near the top, MA-1 has only partial ANE, less than Kalash. And what is Asian Steppe Invader?

As far as I have understand. Mal'ta is not taken as proxy for ANE but he was one of the first to have been mixed with this component. Thats their theory.

MOESAN
14-12-14, 01:23
Malta is the younger fo the 3 "old men": (of women? I don't know for all of the three) BUT he is the FARTHER EAST of them, the 2 others being in Eurasian Russia if I'm not wrong

MOESAN
14-12-14, 01:49
error mistake, sorry
"veteran" Ist'Ushim is around the Urals, not very in middle of european Russia! but it is farther West than Mal'ta (adn less 'North Siberian'-'Amerindian'

ElHorsto
14-12-14, 11:56
Doesn't seem photshopped to me. The yellow background just makes the font more sharp than the darker ones. The font to the right on white background is equally sharp.
And I don't see anything wrong with the angle.

ElHorsto
14-12-14, 12:09
Yes, with better resolution, you're right.

It's a little off in terms of strict correlation with ANE, perhaps because it's a combination signal with both WHG and ANE, and a little of other things as well? ANE for Sardinians is 8%, for Basques it's .114, which is actually a little more than for north Italy, which is .108.


Yes, WHG and ANE are indeed strongly linked, which should not be forgotten. In conclusion, Basques have both, more ANE and more WHG than north Italy. I don't have the numbers at hand but if I remember correctly, even ANE/WHG ratio is higher in north Italy than in Basque country.



Look at this old Cavalli-Sforza map based only on blood proteins:
http://www.bmanuel.org/corling/euIt_comp3++_.jpg (http://www.bmanuel.org/corling/eur_comp3++_.jpg)

Unfortunately, Sardinia isn't included.

This map does not fit ANE admixture well. It rather matches the R1a distribution or the satem-speaking groups.

Greying Wanderer
17-12-14, 11:45
That reminds me, Genetiker made a post where he computed the frequencies of the SNP most strongly associated with blue eyes for many different populations here: https://genetiker.wordpress.com/2013/06/01/frequencies-for-blue-eyes-snp-rs12913832-in-hgdp-populations/

And apparently, for the Karitiana (an isolated south American tribe) 34.6% of them have at least one G, and 7.7% of them have both G's. And the G allele is present in lower frequencies in some other Amerindian tribes.

I wouldn't have thought that something like 7.7% of the Karitiana would have blue (or green) eyes - at least, I've never heard of any of them with that trait - although I could be wrong. Maybe there are other genes that Europeans have that influence having blue eyes, that are lacking in the Karitiana.


That sounds like a possible clue.

edit: now I think of it I remember reading about a north American tribe said to have or to have had lots of grey/green eyes. Will try to remember the name.

http://en.wikipedia.org/wiki/Mandan