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Thursday, November 6, 2014

Kostenki14: first genome of an Upper Paleolithic European


At last, we have an ancient genome from pre-LGM Europe: Kostenki14 (K14) from the famous Kostenki Upper Paleolithic site in southern Russia. The paper, Seguin-Orlando et al. 2014, is locked away behind a paywall, but at least the supplementary materials are open access.

K14 is dated at 38,700-36,200 cal BP and belongs to Y-chromosome haplogroup C-M130, a basal and widespread paternal marker that has already been reported in three other ancient European genomes: La Brana-1 from Mesolithic Spain and NE5 and NE6 from Neolithic Hungary. It also belongs to mitochondrial (mtDNA) haplogroup U2.

The shared drift stats of the form f3(Mbuti;K14,X), where X is the test population, reveal that from among present-day Eurasians, this early European is most similar to Northeast Europeans, such as Lithuanians, Estonians and Belarusians, and some Western Europeans, like Basques and Orcadians (ie. people from the Orkney Isles). This is also what we've seen from other indigenous European hunter-gatherer genomes sequenced to date.


As far as Eurasians are concerned, Papuans and Melanesians are the most distinct from K14, somewhat paradoxically so, considering the ancient genome's Oceanian-like Y-haplogroup. The authors speculate that this might be because they carry ancestry from a very basal lineage that went its own way before the split between West Eurasians and East Asians. But I'm wondering whether this result can't simply be explained by the inflated Denisovan admixture among Oceanians (usually reported at around 5%)?

Indeed, there's no mention anywhere in the paper that K14 has Denisova ancestry. However, much like the recently published Ust'-Ishim genome, it shows significantly larger genomic tracts of Neanderthal origin than present-day Eurasians. The implication of this is obvious, and well covered elsewhere, so I won't go into it here.

Arguably the most controversial outcome of the study is that it shows K14 to be partly of Basal Eurasian origin. This is a highly divergent Eurasian clade first described in Lazaridis et al. (see here), and associated with Neolithic farmers. Seguin-Orlando et al. came to their conclusion via two sets of D-statistics and an ADMIXTURE run, which showed K14 to carry a component specific to the Middle East.

If true, then this finding debunks one of the main premises in Lazaridis et al., which is that Basal Eurasian admixture first arrived in Europe from the Middle East with Neolithic farmers. However, it doesn't debunk this paper's model of the formation of the modern European gene pool. Basically, for that to happen we'd need the Basal Eurasian component to show up in pre-Neolithic samples from Western and Central Europe.

Nevertheless, David Reich (one of the co-authors of Lazaridis et al.) seemed so taken aback by the news that he suggested K14 might be contaminated. Or at least, he was reported to have made this suggestion (scroll down to the last paragraph here)

This is interesting because Reich is currently working on a paper that includes ancient genomes from the Samara Valley, which isn't too far away from the Kostenki site (see here). Judging by his reaction to K14's purported Basal Eurasian admixture, we can probably assume that the pre-Neolithic genomes he's analyzed from Russia don't show any signals of this type of ancestry.

In any case, the model devised by Seguin-Orlando et al., set out in the figure below, is actually very similar to the one in Lazaridis et al., with NEOL basically standing in for EEF (Early European Farmer) and MHG for WHG and SHG (Western European Hunter-Gatherer and Scandinavian Hunter-Gatherer, respectively).


However, the suggestion that the Yenisei Siberians carry MHG rather than ANE doesn't look right to me. Why would Siberians carry European rather than Siberian hunter-gatherer ancestry? I suspect the problem is that MHG is a composite of WHG and ANE (because, as we know, SHG are partly ANE). Thus, if the Yenisei Siberians do carry both ANE and WHG, because they might indeed harbor some ancient European admixture, then perhaps this is simply being classified as MHG? If so, then I suppose it's not technically wrong, but it does look confusing.

Citation...

Seguin-Orlando et al., Genomic structure in Europeans dating back at least 36,200 years, Published Online November 6 2014, Science, DOI: 10.1126/science.aaa0114

241 comments:

1 – 200 of 241   Newer›   Newest»
Matt said...

Davidski: It's apparently closely related to both ANE and WHG

Equally related to both, and more related to both than they are to one another - it's a hybrid?

Equally related to both, but exactly as to both or less related to both than they are to one another - it's an outgroup?

What the full paper shows with respect to these two options is pretty unclear from the press releases. The supplement's Treemix tends to show Kostenki as either co-equally an outgroup as MA-1 to Mesolithic Europeans and West Eurasians (and an instantaneous split with MA-1), or an outgroup to West Eurasians, Mesolithic Europeans and MA-1. No signal of MA-1 plus WHG clade admixture.

Davidski said...

I just got a headache when looking over the supp info PDF.

But what I find intriguing is that David Reich suspects this genome might be contaminated, because he's seen Mesolithic genomes from the Samara Valley, which is pretty close to the Kostenki site.

Roy King said...

I am concerned that there may have been Mesolithic people who are similar to Kostenki, namely, having Near Eastern autosomal components, long before the arrival of Neolithic farmers, possibly Mesolithics in Corsica, Provence or Sicily or even Sardinia. If true, the actual Neolithic component in Iceman or Stuttgart would be striking less than what we assume and there similarity autosomally to Sardinia would be an artifact of persistent Paleolithic/Mesolithic genetic markers. (reposted from previous discussion)

ZeGrammarNazi said...

The Y-DNA results are interesting and make C6/C1a2 the front runner for the aboriginal European lineage. We have evidence now of C6/C1a2 being present from the Upper Paleolithic through the Neolithic.

I know it is almost non-existent today in Europe, but I wonder where it most frequent anyways?

terryt said...

"I know it is almost non-existent today in Europe, but I wonder where it most frequent anyways?"

European C-V20 is, as you say, labelled C1a2 at ISOGG. C1a1-M8 is a Japanese/Ryukyu haplogroup and not especially rare there. In other words C1a was probably widespread across northern/central Eurasia at some ancient time. Other C1-F3393 haplogroups are 'southern': C1b1-M356 Western India and Bangladesh, C1b2-M38 in Eastern Indonesia and C1c-M347 in Australia. C2-M217 is East Asian.

ZeGrammarNazi said...

@ terryt, I was familiar with C1a1 being present in Japan, and already assumed C subclades were spread throughout Eurasia before other y-lineages moved into their areas.

I was not aware of the other subclades you listed, though. Thanks for that.

Roy King said...

What if Kostenki mirrors the Southern Route OOA (Y Haplogroup C) and Ust'Ishim the Northern route (K(xLT) on the way to NO)? That would explain Kostenki's U2 mtDNA and Ust'Ishim's mtDNA R as well). Marta Lahr was an original proponent of the Southern route and Kostenki does have autosomal characteristic of ASI--Southern India. Perhaps Europe has been influenced by both streams in the Upper Paleolithic.

Grey said...

"Equally related to both, and more related to both than they are to one another - it's a hybrid?"

Could it be parental to both or is that not possible?

.

"I am concerned that there may have been Mesolithic people who are similar to Kostenki"

If "basal" was originally very widespread and the first farmers developed out of one cluster before they expanded then might some clusters of WHG have the same signal confusing the issue in some areas?

.

"in Corsica, Provence or Sicily or even Sardinia"

It may not be relevant to this but I wonder about malaria protection acting as a kind of dna pickling mechanism i.e. ancient dna surviving in clusters in what used to be swamps because the original population had malaria protection and so they weren't swamped by later waves.

Davidski said...

One of the authors thinks that MA-1 carried admixture from the Kostenki 14 population:

"For example, the genome reveals that the people from Kostenki contributed genes to the ancestors of the boy from Mal’ta, who lived in Siberia 26,000 years ago, and whose descendants spread as far as Europe and the Americas."

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

How'd he work that out?

ryukendo kendow said...

Hey guys, I have access to the paper, so AMA.

Here are the main conclusions:
1) Kostenki (K14) shows the most similarity with WHG and lesser with modern day Europeans.
- The greatest affinity by f3 is with loschour, and secondarily with La Brana and Scandinavian HGs.
- The greatest component in ADMIXTURE for K14 is shared with N. and E. Europeans.
- f3 stats show the most affinity with Europeans.
- For pairs of pop incl. European and East Asian, K14 is closer to European.
- f3 results are robust to contamination.

2) All pops other than Oceanians are closer to WHG samples or MA-1 than to K14.
3) ADMIXTURE shows K14 share some protion of a component in Neols and Near Easterns.

4) From 2) + 3), K14 had basal Eurasian.
- East Asian equally distant from K14 and Stuttgart using D-stats (!)

5) Siberians from the Ob and Yenisei closer to European than to K14, but closer to Scandinavian WHG than to European, and closer to Scandinavian WHG than to Mal'ta. The best mix not European + Even Siberians, or Mal'ta + Even Siberians, but Motala + Even Siberians, implying early gene flow prior to Mesolithic.

6) K14 has higher Neanderthal segment length than modern pops and later aDNA. Authors draw same conclusion as those for Ust-Ishim, aka 54kya, OOA.

7) Restricting 'analysis to areas without evidence for neaderthal-introgressed haplotypes in contemporary humans results in 0% estimated ancestry for most individuals except K14, where 0.9+-0.4% Neanderthal ancestry is still detected.' Authors attribute this to selection out or drifting out of neand till modern times, or further neand input into K14. No evidence for introgression from other unknown archaics.

8) 'Our results show no close genetic relationship between K14 Australo-Melanesians, and support earlier studies that Australo-Melanesians derive part of their ancestry from an early population divergence that pre-dates the separation of Europeans and East Asians' (!)

ryukendo kendow said...

Preliminary observations:

I) East Asian are equidistant to Stuttgart and K14. This implies that K14 has as much ancestry from an outgroup to (ANE-WHG-ENA) as Stuttgart does, or at least has a lot of it. This is compatible with 1) because the ADMIXTURE run does not create a pure WHG or pure Basal component, so the N-Euro like component probably hides some basal ancestry in K14.

II) Native Americans are closer to K14 than Stuttgart is. However, K14 is not closer to NAms than to East Asians. I think this means that the crown eurasian portion of K14 is very basal WHG, though of course error bars and whatnot might just mean over-interpretation.

p.s. I predicted some time ago that Crown Eurasian vs Basal Eurasian won't be the whole story, and that Oceanians had some extremely basal input, just that we don't know where that diverges. It appears the paper confirms this.

@ Davidski
I requested for some treemixes where we would try to get some 'basal-like' edges into Oceanians that were not Denisovan. This paper does produce such edges, but from the proto-human (!) branch to Papuan. Not sure what the significance is if any.

III) This probably means that later European WHG-ANEs are descended from a branch further east, who either 1) took a detour around K14's position to the North and East, or 2) replaced K14's descendants, and these new arrivals had no basal.

IV) This means that basal populations existed in Eurasia, prob in Middle East, and the Crown Eurasian root has to be further east.

ryukendo kendow said...

Kostenki was mentioned in the discussion just a few days ago from the other article about Ust-Ishim; parasar posted on him over at anthrogenica:

"...Certain cranial features, including very narrow braincase, low and narrow face, marked prognathism (anterior protrusion of the midface), and very wide nose, are typical of tropical populations. The trait combination links the cranium with those of Papuans and Melanesians.

Certain other Upper Paleolithic crania from Europe, too, display “tropical” features. Bodily proportions of Early Upper Paleolithic people reveal southern characteristics as well. This also concerns the arm proportions of the Markina Gora individual, whose forearm was relatively long compared to the shoulder.

The meaning of those facts is yet unclear. Modern geographic human groups (so called “races”) had not completely formed by the Upper Paleolithic, and some of their characteristics may have incidentally appeared in various parts of the world."

"M.M. Gerasimov, like G.F. Debetz, believed that people of such appearance or their direct ancestors had actually migrated to Europe in the early Upper Paleolithic from areas lying far south. Therefore he endowed the reconstructed individual with tropical characteristics including curly hair. The future will hopefully show whether or not this “artistic liberty” of the scientist and sculptor was warranted."

http://www.kunstkamera.ru/en/temporary_exhibitions/virtual/gerasimov/09

It seems that early pops in temperate Eurasia all had a rather undifferentiated 'Papuanoid' morphology, pointing to tropical origins in recent periods.

barakobama said...

"One of the authors thinks that MA-1 carried admixture from the Kostenki 14 population:"

Eske Willerslev in that video seems to be saying that the same basic people("meta-population)" lived from Europe-central Asia for a span of at least 30,000 years, who "exchanged genes in a very complex network and it's not this massive movement of people all the time going back and forth."

I think he may mean ANE and WHG are of the same branch, which had descendants who mixed and diversified for a span of 30,000 years. ANE and WHG may not be cut-and dry pure populations.

The most interesting thing to me is that all of the ancestral components that make up modern west Eurasians already existed in Russia as far back as ~37,000 years ago and that there was population-continuum from central Asia-Europe for over 30,000 years. K 14 should be considered as a very very very very very early west Eurasian.

Europeans and west Asians(i guess there's some Sub Saharan) can be fit as a mixture of ANE-WHG branch and basal Eurasian. Hopefully there's a way to learn about what was happening in west Asia before the Neolithic looking at modern variation.

barakobama said...

Ryu, would you say that K 14(minus non-"crown Eurasian") is from the same branch of WHG and ANE, but had already split with WHG away from ANE? Or is it not that simple?
It's very interesting that K 14's relationship to modern pops seems to mirror WHGs, and overall he's closest to WHGs. This has to mean his people went deep into Europe and are somehow ancestral or closely related to WHGs.
I think we should all take this speculatively, and just say what is most likely. It’s amazing that there are already three Upper Paleolithic genomes from mainland Eurasia.

Davidski said...

rk,

Aren't the admixture edges running from the Denisova branch to the Papuans the same 5% or so Denisova ancestry in Oceania that we've seen before?

ryukendo kendow said...

Also, the fact that West Eurasian introgression into Siberians from the Ob-Yenisei requires 1) a West Eurasian Population that has no basal, thus no modern Europeans, 2) something that is not too ANE-rich like Mal'ta, 3) a conbination of WHG and ANE like Motala so far east in Siberia, means that the situation in Siberia must have been very complex.

The authors postulate pre-mesolithic gene flow, but another scenario is that Mal'ta like pops retreated to the south in the steppes after the Mammoths died, and WHG-rich HG pops with a more conducive lifestyle expanded East to meet the Siberians in the forest that grew after the ice went.

Lastly, I might be wrong on this; it looks to me that the fact that Euro pops are much closer to Stuttgart and Loschour than to K14, despite the 1) extremely high basal in Stuttgart and 2) K14 having a similar WHG-Basal mix as present-day Europeans vs Loschour, prob means that the WHG in stuttgart and loschour forms a clade with the WHG in current-day Euros to the exclusion of the WHG in K14.

ryukendo kendow said...

@ Davidski
Fig S25 shows something new.

@ BarakObama
1) If he were an outgroup to WHG-ANE, then modern Euros and NAms will be closer to Louschour and Mal'ta than to K14, and East Asians will be equi to Loschour, Mal'ta and K14. But East Asian are closer to Loschour and Mal'ta than to K14.

2) If he were on the branch leading to ANE, then NAms will be closer to K14 than Loschour, and East Asians will be equi to k14 and loschour, but this is not the case.

3) This leaves us K14 on the branch to WHG. However, K14 cannot be pure WHG, because all crown eurasian pops are closer to Loschour than K14 is. So K14 is admixed WHG, with basal from Near East most probably.

One way to confirm this would be to run f3 stats across all pops modelling K14 as a combination of 2 genomes. If the authors are correct the best result will be something like Loschour+Bedouin or such. Hey David, can you try this once the genome is out?

Davidski said...

rk,

S25 shows the same phenomenon, but it looks slightly different, with the admix edge coming off the branch leading to Denisova and the Neanderthals, probably because Kostenki14's Neanderthal admix and low coverage are being misinterpreted as Kostenki-related gene flow into the Neanderthal branch.

ryukendo kendow said...

There's one possibility I missed, and that is:
4) K14 is BOTH an outgroup to ANE and WHG, and K14 is admixed. This would make K14 equi to Mal'ta and Loschour, but he is closest to Loschour and Brana to the exclusion of Mal'ta.

All these are with the assumption of tree-like splits.

ryukendo kendow said...

@ David
So we focus on the last image in the sequence? Do you think the 'mistakes' Treemix makes at lower variance explanation have any significance?

Eduardo Pinto said...

@ ryukendo kendow


"...Certain cranial features, including very narrow braincase, low and narrow face, marked prognathism (anterior protrusion of the midface), and very wide nose, are typical of tropical populations. The trait combination links the cranium with those of Papuans and Melanesians.

Certain other Upper Paleolithic crania from Europe, too, display “tropical” features. Bodily proportions of Early Upper Paleolithic people reveal southern characteristics as well. This also concerns the arm proportions of the Markina Gora individual, whose forearm was relatively long compared to the shoulder."




That reminds me of the Muge shell middens - http://www.tandfonline.com/doi/abs/10.1080/15564891003638184#.VFxdK4WvjFU- description written by Mendes Correia in 1924.
I know you probably don't understand Portuguese but you'll get the sense of it...

"É um tipo que tem caracteres negróides (...), alguns australóides (...) e mesmo uma estatura baixa, aproximando-os dos pigmeus africanos. Dos tipos quaternários da Europa, seria o proto-etiópico Homo aurignacensis o que com ele mais semelhanças possuiria ..."

ryukendo kendow said...

Reconstruction by Gerasimov.

http://www.donsmaps.com/images8/kostenkihead.jpg

Davidski said...

rk,

I've seen similar admixture edges from the Denisova/Neanderthal branch to the Oceanians in my own runs, but didn't think these were anything but the usual signals of Denisova-related ancestry in Oceania.

TreeMix shows a lot of weird stuff if the experiments are too complex or aren't set up right.

ryukendo kendow said...

@ Davidski
Just to confirm we are referring to the same thing: I'm looking at the first two figures in S25, which show a branch from proto-human to Papuan, not from proto-neand to Papuan.

Point taken though.

Now that we have some papers saying this too, do you think there is any way to find out, using the tools we have today, what divergent group contributed to Oceanians and where they branch off?

Davidski said...

Yes, the start point of that admixture edge tends to jump around like that. In some of my tests I've even seen an edge from near the Mbuti to Papuans. But I haven't been able to split this signal into Denisova and something else further up the tree. So I don't know how to confirm what it is apart from the usual Denisova-related gene flow being mis-interpreted by TreeMix?

By the way, where's this genome stored? Felix was asking for the link.

ryukendo kendow said...

@ Davidski
I didn't see it. Where does it usually say?

BTW, here are three figures from the paper.

http://imgur.com/TWdW0wi,DuOEx4K#0
http://imgur.com/ckIseY9

ryukendo kendow said...

"We also note that the tree is not the result of a model-fitting procedure, but rather a possible topology consistent with the key results of this study."

With regard to exactly where K14 is in ANE-WHG:

"An interpretation of the above results would be that K14 is an early member of a lineage leading to western Eurasian MHGs, after their split from the proposed ancestral northern Eurasian lineage including MA1. However, D-statistics of the form D(Mbuti Pygmy, Modern; Ancient, K14), which test whether K14 and an ancient individual form a clade with respect to a modern population, reject this simple tree-like relationship. We find that all contemporary non-Africans, except Australo-Melanesians, are closer to either Mal’ta (MA1) or MHGs than to K14 [e.g., Z = -5.3, for D (Mbuti, Han; Loschbour, K14); SOM S9; table S10; fig. S19]. This would suggest a basal position of K14 with respect to MHGs and ancient north Eurasians, which is also shown in admixture graphs using TreeMix (SOM S12; fig. S24 and S25). In addition, a sizeable component of K14’s ancestry observed in the model-based clustering analyses is predominant in contemporary Middle Eastern/Caucasus (ME/C) populations and Neolithic ancient genomes (NEOL) (Gok2, Iceman, Stuttgart), but absent in MA1 or MHGs (Fig. 1B and fig. S20). This component has been associated with a suggested “basal Eurasian” lineage contributing to NEOL, to explain an observed increase in allele sharing between MHGs / MA1 and East Asians compared to NEOL (21). Since K14 shows the same pattern as NEOL, a parsimonious explanation would be that K14 also derives some ancestry from a related “basal Eurasian” lineage. Consistent with this hypothesis, we find that East Asians are equally distant to NEOL and K14 using D-statistics as described above."

Matt said...

Davidski But what I find intriguing is that David Reich suspects this genome might be contaminated, because he's seen Mesolithic genomes from the Samara Valley, which is pretty close to the Kostenki site.

Those are always concerns. It's tough for me to understand the technicalities of contamination procedures. Where these interface with relatedness, my assumption with contaminated samples is that like Afontova Gora sample (contaminated right?) should be closer to modern people, while K14 seems more distant.

Contamination from a Russian source would probably also move the sample more in the direction of Russians, and that doesn't seem to be the case – although if it is the case, then I guess we dial back our confidence in our assumptions about its differential closeness to Russians and Russian like peoples a bit.

The genomes Reich has seen are from a spatially relatively close place, but after 20,000 years. Unless any of his project's samples are near that early? Could be a lot of population replacement / mixing with more “West Eurasian” populations from the East by then (giving rise to “WHG”), following glaciations marginalising territory where a European Upper Paleolithic type mix of mostly West Eurasian, minority BE peoples could live...

RK This leaves us K14 on the branch to WHG. However, K14 cannot be pure WHG, because all crown eurasian pops are closer to Loschour than K14 is. So K14 is admixed WHG, with basal from Near East most probably.

Although if K14 is “just” WHG-BE mixed, I think it should also be closer to Stuttgart than Loschbour is. And should be closer to Loschbour than MA-1 is.... Doesn't seem to be the case on dendrograms.

IMO Kostenki is an admixed BE-West Eurasian population that within West Eurasian has some differential relationship to WHG compared to ANE, but not very much, and by the time of the Mesolithic, with the most remnants in La Brana and Southwest European WHG.

ryukendo kendow said...

Oceanians are closer to Kostenki than to Stuttgart, and closer to Kostenki than to Mal'ta or Loschour. This is very weird to me.

Furthermore, K14 behaves like papuans or South Asians and unlike all other Eurasians, by scoring non-noise level of African at low K.

Matt said...

@ RK “http://imgur.com/ckIseY9”

Just seen the model you posted up from the paper (thanks), and that basically seems to fit with what my assumptions are with that –

- three way split of the “West Eurasian” (possibly actually Central Eurasian) Upper Paleolithic population
- one branch of which mixes with BE to give rise to UP Europeans
- and the others of which go their own ways, separately to create “WHG” and “ANE”

although I was also thinking there may have been a “metapopulation” or admixture between WHG-ANE or Kostenki and WHG's West Eurasian ancestors for some time, and apparently they don't seem to have modelled it that way. E.g to explain additional similarities between the groups. Perhaps that's because the model simplifies a little, or perhaps because its not there.

ryukendo kendow said...

@ Matt
Agree mostly with that.

This paper does not have comparisons of K14 with Stuttgart and Loschour in a single D test. I have no idea how that would turn out actually. But it does show that K14 is not more related to NAms than to EAsians wrt Loschour, meaning that K14 could not have contributed to ANE, or shared a branch with ANE, any more than Loschour did. K14 is either on the WHG branch or on neither branch.

It also shows that NAms, EAsians and Euros are all closer to Loschour than to K14; this implies some contribution from the outgroup of (WHG-ANE-ENA) to K14. Of course we don't really know what the outgroup is really, until we do some formal modelling, but Basal is as good an exp as any at this stage.

I think the balance of evidence suggests that K14 is more likely to belong with WHG than an outgroup to both, because f stats suggest it is closer to Loschour and Brana than Mal'ta, and an outgroup status would make this difficult to explain. One thing that might change this is if Mal'ta has Han-like ancestry.

We should remember that the reason why this was rejected in the other paper was because Mal'ta are not closer to Han than Loschour are.

ryukendo kendow said...

@ Davidski
I think one easy way to test for Basal in Brana is to see if East Asian and NAms are closer to Loschour than they are to Brana by D stats, in the same way that things are done here.

ryukendo kendow said...

The populations in Siberia closer to Ajvide and Motala + Evens instead of Gokhem or Iceman + Evens are exclusively Uralic populations, plus Kets. This is interesting because Nganassan and Ket typically get their own component in ADMIXTURE at high K, and this is found amongst Uralic pops usually. It is a secondary component amongst Siberian Altaics like Yakut, who get a more East Asian, less Siberian component on top of the Nganassan one.

Uralic expanded from somewhere east, and the easternmost pops of Uralic are more East Asian than the westernmost ones, so this seems to imply that at the time of the Uralic expansion a scandinavian HG-like pop was still living in much of the Taiga, which got overprinted by the oncoming Uralic wave.

Hector said...

Most of these speculations are not of paleontological interest but of psychological and sociological interest.

In the branching model accepted as "true" by most of you, isn't it odd that almost every branch is "West Eurasian"?

Whatever is your disposition toward me, you should find it at least odd.

Chad Rohlfsen said...

Could he just be an intermediary between Ust-ishim and WHG? Not yet fully derived?

DDeden said...

ryukendo kendow said...
"Oceanians are closer to Kostenki than to Stuttgart, and closer to Kostenki than to Mal'ta or Loschour. This is very weird to me."

I wrote earlier that (ancestors of) Papuans & Mamanwa(Phil.) travelled through Central Asia meeting Denisovans and continued to China coast & east rim of SE Asia to Papua. Unlike pygmies(Andaman, Queensland, Flores), they did not follow the Indian Ocean coast eastward from Africa.

Grey said...

@rk

"Oceanians are closer to Kostenki than to Stuttgart, and closer to Kostenki than to Mal'ta or Loschour. This is very weird to me."

Is it possible a Kostenki's pop. were part of an expansion from Oceania which simply hadn't had time to change much from the original source population while Suttgart, Mal'ta etc had had more time to develop adaptations to the local environment?

so
Pop 1) oceanians in oceania
Pop 2) oceanians *in* north eurasia
Pop 3) oceanians *adapted* to north eurasia

.

I wonder about this now as my personal model is a sequence of "Out of" events and originally I thought the most likely sequence was

1) out of the tropics
2) out of africa
3) out of india

(based on surface area ~ effective pop. size ~ probability of developing useful adaptations)

However if it's not so much surface area as total coastline - for fishy reasons - then maybe SE Asia fits the bill better?

.

@barak

"ANE and WHG may not be cut-and dry pure populations."

My little theory on that is the same pop. diverged to adapt to the ecozone they were living on.

(my guess being WHG as a near coastal pop. and ANE as a deep interior pop.)

.

@Hector

"In the branching model accepted as "true" by most of you, isn't it odd that almost every branch is "West Eurasian"?"

Not sure I understand the question but I think the big east-west distinction is the East Asian farmer expansion was much more complete and so a lot of the same kind of distinctions in the east were buried.

John Smith said...

If Koskenki belonged to C, and Ust-ishim belonged to K2a0 does it mean that haplogroup C came from Europe and haplogroup K2 came from Asia?

Grey said...

oceania and se asia used interchangably and randomly in previous post but you prob get the idea.

ryukendo kendow said...

@ Hector
To who?

The ENA branch, with (Papaun-(ASI-Dai)), has more branches than the West Eurasian branch.

@ Grey @ DDeden
However, I think K14, if anything, solidifies support for multiple radiations from India/SEA, because K14 has Basal Eurasian even though it is on the Pontic-Caspian. This implies a route from the South and East, not so far west that lots of ancestry from the middle east comes into play. Also, look at the K14 morphology.

John Smith said...

Did Kostenki belong to the Aurignacian culture? If not what culture did he belong to? I guess this proves that someone in Hawaii would have a direct male ancestor from Upper Paleolithic Europe.

John Smith said...

"Oceanians are closer to Kostenki than to Stuttgart, and closer to Kostenki than to Mal'ta or Loschour. This is very weird to me."
He had haplogroup C for crying out loud of course he is going to have eastern associations. However, his old old almost seems to prove that CxC3 or all C may have origins in the Aurignacian culture

ryukendo kendow said...

@ John Smith

Actually, C6, K14's Haplogroup is not an ancestor to anyone. It is a descendant of C1, which is found in Japanese. C1 is nested in Indian clades.

Hector said...

It is always funny when someone does not see a rhetorical question and awkwardly tries to be sarcastic.

Hector said...

So far I have tried not to be pedagogical but this guys is getting on my nerve.

C6 is not a descendent of C1. No contemporary line is a descendent of another contemporary lineage. All y chromosomes at any given time are roughly equally derived.

In fact any given ancient sample of sufficient age is very unlikely to be a direct ancestor of any modern human beings in a uni-parental line.

John Smith said...

As a matter of fact Kostenki did not even belong to C1 look at this table he lacks the F3393/Z1426 mutation http://snag.gy/HNZjF.jpg.

Hector said...
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Hector said...
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Hector said...

Maybe I need to be cautious. I need to see the top of chart. If "False" means just "no call" I got excited for nothing.

Hector said...

That excuse does not work because you cannot mix old and new nomenclature.

No one says C2-M38 and C2-M217 in the same paragraph.

By the way M38 line and M347 line form a clade according to the new ISOGG tree. So no, these are not nested in India.

ryukendo kendow said...

Not an excuse. I know it's a mistake.

The chart is found in supps. The chart is of all SNPs found. True and false have the heading 'isdamage', which refers not to the prescence of SNPs.

So this guy is definitely less basal than the Malaysian.

There are multiple signs that K 14 moved from the south to his current position, including both y hap (with caveats) and his basal Eurasian.

ryukendo kendow said...

@js
The question here is why oceaneans, of all ENA, have this relationship.

terryt said...

"Now that we have some papers saying this too, do you think there is any way to find out, using the tools we have today, what divergent group contributed to Oceanians and where they branch off?"

For some time now I have thought that Papuans must have admixture with a pre-sapiens SE Asian population. Perhaps that explains the reasonably high Denisova element in them as well. And with Y-DNA K2(xK2a) apparently originating in SE Asia and K2b2 spreading around the world from there we have an explanation for:

"...Certain cranial features, including very narrow braincase, low and narrow face, marked prognathism (anterior protrusion of the midface), and very wide nose, are typical of tropical populations. The trait combination links the cranium with those of Papuans and Melanesians".

"C1 is nested in Indian clades".

Not really. There are three C1 clades currently recognised. C1b is the only 'Indian clade' and it has just one of two branches confined to that region, the other being found in Eastern Indonesia. C1a has been found in both Japan and Europe and C1c is confined to Australia. Whether C1 as a whole moved east or west is an open question at present, although C2 is very much an eastern haplogroup.

"As a matter of fact Kostenki did not even belong to C1 look at this table he lacks the F3393/Z1426 mutation"

Interesting. It makes sense as I have long suspected Y-DNA C moved east through Central Asia with that link being broken during climate deterioration. Looks as though both C and K2 had early representatives through the northern half of Eurasia whose line became extinct.

"What if Kostenki mirrors the Southern Route OOA (Y Haplogroup C) and Ust'Ishim the Northern route (K(xLT) on the way to NO)?"

If the above holds the movements would be the other way round with C following a northern route and K a southern.

Hector said...
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Grey said...

"The question here is why oceaneans, of all ENA, have this relationship."

My guess (just based on the possible logic behind it) is an expansion from a source region in SE Asia to both Oceania and elsewhere (including Kostenki). Source region later swamped by eastern farmer expansion but not as far as Oceania leaving it as an remnant.

Hector said...
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Hector said...
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Hector said...
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Grey said...

I keep wondering if Cillian Murphy is C

http://images4.fanpop.com/image/photos/19900000/Cillian-Murphy-cillian-murphy-19924487-532-600.jpg

(not likely but i'm still curious)

John Smith said...

@Hector what evidence do you have that Kostenki belongs to C1 all I have is this table which suggests he belongs to C but not C1 http://snag.gy/YCafp.jpg. I want to know what Kostenki belongs to I don't care if its C1 or C*.

John Smith said...

Oh, I guess the true/false is irrelevant in that table if that is the case than he does belong to C1
http://snag.gy/eNbMy.jpg.

Hector said...
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ryukendo kendow said...

@ JS

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

Go to pg 78. Look at what True, False actually means.

@ Terry

Hmmm, Why do you think that C took a different route from K?

C seems to mirror K in many ways. 1) Basal C in SEA+India, plus one pan-Eurasian clade and one ENA clade. 2) One northern offshoot from aDNA caught in the act of moving north and grazing the middle east en route. 3) Don't the same autosomal issues about the difficulties of reconciling migration north of the himalayas down to Australasia with the (WHG-ANE)(Oceanian(ASI-Dai)) branching apply to both K and C?

It seems that autosomal splits at the intercontinental level, e.g. basal vs crown or within-crown splits, are reasonably tree like; this implies to me at least that complex crisscrossing movements across east Asia with clockwise and counterCW movts around the himalayas at such an early date is kinda ruled out.

@ Grey
The weird thing is, why didn't this affinity also pass itself on to East Asian farmers?

One way is to postulate something that contributed to both K14 and Oceanian, pulling them away from Stuttgart, while Dai and French are surprisingly closer to stuttgart.

Pure speculation: This thing that contributes would have to be outgroup to (Basal(Crown Eurasian)) due to stuttgart, and will be extremely divergent indeed. K14 score in African, like papuans, and this African does not diminish at higher K when Papuans get their own component. Also the authors conclude that something diverging outside of European and East Asian is going into Papuan.

ryukendo kendow said...

Wait.
This paper has a glaring ommision: it does tell us anything about Denisova introgression into K14.

Denisova is not even mentioned in the full text. In the supplementary material Neanderthal introgression and 'introgression from unknown unsampled archaic hominins' is formally worked on with results presented, with the former similar to U-I and the latter ~0%, but the work that is done on Denisova is not presented...

Not sure how significant this is, but in light of the weird stuttgart findings and the oceanian exceptions, I'm suspecting another paper...???

terryt said...

"Hmmm, Why do you think that C took a different route from K?"

Several reasons. 1) There was some basal separation between C and F which I assume was originally geographic. 2) It also seems reasonably obvious that mt-DNAs M and N followed different routes east, probably originally accompanied by separate male lines. 3) F's diversity, especially that of the IJK branch, seems to follow a sequential diversification from west to east through South Asia, and is well represented there. 4) C on the other hand is not common in India and basically confined to Bangladesh and Gujarat, possibly as a result of following a Ganges and Indus River route through the region. 5) It is extremely difficult to imagine a scenario where C2 forms a separate branch from C1 in East Asia having moved through South Asia first, whereas it's easy to imagine a separation between C1 and C2 in East Asia with C1c having formed in Australia, C1b in SE Asia/India and C1a emerging from South Asia onto the Eurasian steppe and expanding through that region.

"C seems to mirror K in many ways. 1) Basal C in SEA+India"

Well no. Basal C is probably East Asian/Se Asian/Australian. Basal K is SW Asian.

"plus one pan-Eurasian clade and one ENA clade".

I agree the expansion od C1 and K2b2 are quite possibly closely connected.

"One northern offshoot from aDNA caught in the act of moving north and grazing the middle east en route".

Fits what I suggested above for the Y-DNA.

"Don't the same autosomal issues about the difficulties of reconciling migration north of the himalayas down to Australasia with the (WHG-ANE)(Oceanian(ASI-Dai)) branching apply to both K and C?"

I think you make a mistake in not differentiating between 'Australian' and 'Papuan' genetic histories. Their haplogroups are reasonably distinct although with some overlap. An Australian origin through a northern movement fits the old idea of Kostenki being 'Australoid'.

"The weird thing is, why didn't this affinity also pass itself on to East Asian farmers?"

In response to Grey:

"My guess (just based on the possible logic behind it) is an expansion from a source region in SE Asia to both Oceania and elsewhere (including Kostenki). Source region later swamped by eastern farmer expansion but not as far as Oceania leaving it as an remnant".

If, as I suggested above, the Papuan population became mixed with a pre-sapiens SE Asian population then the K2a branch would have missed it as that branch didn't reach as far south as the other K2 branches. That means that when O expanded it lacked the Papuan element.

ryukendo kendow said...

@ Terry
Thanks for your answers. I agree that paring it down to K2 and C1 seems to make sense.

A few questions:
1) Where was the basal K found?

2) Do you think Y-haps are as reliable as autosomal for the Australia vs Papua case, or for that matter any case?

The Y-chrom is basically one big haploid genetic unit subject to rapid drift, basically a single, rapidly mutating allele; while the rest of the genome is not like this. It seems like Oceanians are basically on the same place in the tree wrt to all other populations, Aust+Pap branching off only from each other autosomally with little/no gene flow from anyhwere else later, implying that their different Y and MtHaps are due entirely to drift.

3) It seems like the same argument can be used for C in India. There is no D in India, but we know there must be in the past because Onge behaves in a tree-like manner wrt ASI and split of ~24000 ya from ASI, with no real gene flow from the mainland after, so there must have been D in India at the time, but D drifted out.

It seems much safer to say that Y-haps are concordant with autosomal movements, and then postulate loss of Y-haps, than to postulate autosomal movements on the basis of Y-haps, because autosomal influx is almost impossible to drift out entirely even if the input is tiny, e.g. neand.

I would like to propose an alternative, simpler scenario, that the Basal Eurasian pop probably carried only E, G, F, with other F, IJK+C+D all with the Crown Eurasian pop in a tropical-subtropical refugium in the Indomalaya Ecozone, with the colonisation of temperate areas in the west by K2 picking up IJ as they moved West.

terryt said...

"1) Where was the basal K found?"

Depends what you call 'Basal K'. I would think IJK formed in Anatolia or Iranian Plateau from basal F. G and H2 also look to have first formed there. KLT probably formed in South Asia, with LT forming from a branch left behind when K2 entered Yunnan/Burma. H looks to do much the same with H1 in South Asia and H3 in SE Asia (I'm not actually sure of that last). 'F' also has a East Asian representative, F2.

"2) Do you think Y-haps are as reliable as autosomal for the Australia vs Papua case, or for that matter any case?"

No. As soon as an individual carrying a particular haplogroup has offspring with someone from a different population with a different haplogroup the a-DNA is halved. And carries on being halved for every following offspring. Y-DNA and mt-DNA are each just one 'gene' amoung many, although they do behave much like other genes in that they spread with selection. But that selection need not be genewtic if some cultural or technological advantage is passed along with the haplogroup.

"It seems like Oceanians are basically on the same place in the tree wrt to all other populations, Aust+Pap branching off only from each other autosomally with little/no gene flow from anyhwere else later, implying that their different Y and MtHaps are due entirely to drift".

I don't think 'drift' explains it. New Guinea has a variety of K2b1 haplogroups while Australia has just the one derived K2b1a which it shares with New Guinea. Australia has a basal branch of C1 while New Guinea has just the Wallacean C1b2a, most of which is coastal and probably associated with the Austronesian expansion. Mitochondrial DNA is similarly split with several basal N branches in Australia and only R-derived branches in New Guinea. Confusing the issue is both have different basal M branches. To me the haplogroup distribution fits a sequential crossing entry from Timor/eastern Indonesia with Australia being settled first (Y-DNA C, mt-DNA N) and the following movement dodging already-occupied Australia and moving along its north coast to eastern New Guinea (Y-DNA K2b1 and mt-DNA P).

"3) It seems like the same argument can be used for C in India. There is no D in India, but we know there must be in the past because Onge behaves in a tree-like manner wrt ASI and split of ~24000 ya from ASI, with no real gene flow from the mainland after, so there must have been D in India at the time, but D drifted out".

D need never have been in India. The Andamans were obviously not settled by the first wave of 'coastal migration' from Africa (24,000 years seems reasonable for their settlement), but settled from the nearby Burmese mainland. I think D moved south from East Asia/eastern Tibet and mixed with a South Asian population in Burma before moving to the Andamans.

barakobama said...

I finally got my 23andme results back today. Surprisingly like my uncle, I have an ancestral allele in some major light-skin mutations(most notable rs16891982), even though I'm only ~5% non-European.

ryukendo kendow said...

@ Terryt
If a WHG person reproduces with another WHG person, his contribution is halved, but both mother and daughter retain the same tree topology wrt to ANE, and we only need the autosome of a single individual to prove this. If a cross-cutting introgression happens with ANE we can detect this even if its extremely diluted in the descendants. This is not really the case for Haploid genetics.

In the case of Papuan and Australian, this means that any contribution from an Eurasian group has to contribute to both, judging from the current tree shape. Agree that a scenario of complex pop movement within the sunda shelf on the other hand might do well to explain the different distr of haps.

Autosomal calcs actually show a much older date of divergence for Andamans than 24000, which is the youngest possible age, the oldest is 34000. The rare haploid connections that tie Onge to the mainland in the last 24000 years lie in india, not in SEA, and Onge have no sign of ANI. This prob means that Onge never interbred with pops that would change their tree topo in any way, incl east asians; they prob only had conection with ASI groups.

Mike Thomas said...

@ many "Equally related to both"

Or more like we need to revise / update our base model ??

Mike Thomas said...

what do we think the timing of C compared to *K is ?

Davidski said...

Does anyone actually know which clade of C K14 belongs to?

I'm not asking for anyone's hopes and dreams, just what the current consensus is based on the available information.

barakobama said...

Ryk, if K 14 is ancestral to WHG(besides having some BB), why are Sardinians more related to MA-1? K 14 may be closer to Loschbour than to MA-1, but if Loschbour closer to K 14 than to MA-1?

barakobama said...

Ryk, also Native Americans are closer to K 14 than middle easterns are(excluding Caucasus). The order of his closest relatives seems to be in perfect correlation with ANE+WHG.

ryukendo kendow said...

@ Davidski
Here:
http://imgur.com/ZZBm1On,6o4MfAz#0

He has P255, V183, V199 & V232 for C, and F3393 for C1.

Full text:
"The Y-chromosome belongs to haplogroup C M130, the same as in La Brana."

Supp material:
".. 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..."
"Results or both of these 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. 13). Furthermore, K14 carries the derived allele for four hg C mutations in ISOGG (p255, V183, V199, V323)(Table S6). The MHG individual from La Brana (22) carries the same derived mutations, suggesting that both are members of a closely related lineage within C."

C1 is probably sure, but we need more resolution+more snps for anything more specific.



@ Barak
Whether loschour is closer to MA1 or to K14 is not tested. However, all Eurasian pops, incl. ENA, are closer to MA1 and Loschour than to K14, which is exactly the same pattern as Stuttgart. E.Asians are equi between Stuttgart and K14, oceanians are closer to K14 for some reason.

Also, f3 stats for affinity alone does not constitute a means to discover exact ancestry.

I have no idea what would happen if we tested Stuttgart with Loschour and K14. The WHG in Stuttgart and Loschour prob form a clade excluding the WHG in K14, but the basal in K14 forms a clade with the basal in Stuttgart excluding Loschour. Uninformative probably.

"Why are sardinians more related to MA-1."
I think this is the reason why the authors left the model as it is, even though they wrote 'f3(Mbuti; K14, X) maximised with MHG(WHG)' in the diagram.

Davidski said...

OK, thanks, I'm reading the paper now.

Tobus said...

@ryukendo:
Native Americans are closer to K14 than Stuttgart is

I seriously doubt that and can't see anything in the paper that would indicate it - what makes you think that?

Oceanians are closer to Kostenki than to Stuttgart, and closer to Kostenki than to Mal'ta or Loschour. This is very weird to me.

Firstly, the MA-1/Loschbour f4s are negative, indicating that Oceanians are in fact closer to MA-1/Loschbour than to K14, not the other way round. And secondly, this paper includes f4 stats that aren't statistically significant, and would have been left out or flagged as such in earlier papers. The original f4 spec said the stat must have |Z|>3 for it to have significance, but I note that the UI paper uses |Z|>2. These Oceania/Stuttgart/K14 results fail to meet this criteria (Z=0.9/1.4/1.9) so while it is weird, it's quite possibly noise rather than a genuine affinity.

This paper has a glaring ommision: it does [not] tell us anything about Denisova introgression into K14.

I'm assuming that omission just indicates there was zero Denisovan introgression.

Grey said...

@ rk

1) "The weird thing is, why didn't this affinity also pass itself on to East Asian farmers?"

2) "This paper has a glaring ommision: it does tell us anything about Denisova introgression into K14."

I don't claim to understand this fully but some things I find odd are:

Why do San and Chinese have eye folds and Papuans don't.

Why do Ainu look like a lighter skinned cross between San and Papuans?

There are no doubt lots of possible sensible explanations but I wonder if the Denisovan admixture was into an older human layer and it conferred an advantage over a later human layer allowing the mixed older layer to expand over the top of the later one.

say
A) Tropical Africa

B) Out of the tropics and out of Africa mostly coastal

C) One pop. somewhere in the sub-tropical zone (my guess India-SE Asia somewhere) develops an advantage and expands outwards over-writing the B population in most places (but not all).

D) One B pop. in East Asia, inland, maybe up some mountains like say the Himalayas, close to surviving pre-humans pick up some useful genes from them that confers a significant advantage allowing them to expand outwards over-writing the C population in the majority of East Asia in a radius around the core source region.

so the sequence in core East Asia going:

B -> C -> B+Den

as opposed to the west going:

B -> C -> whatever


.

I also wonder if fish were a critical enough part of early human diet to make interior regions a population sink until they had specific adaptations to compensate and I wonder if something related to that may have been what they picked up from the Denisovans.

That's a separate thing though.

Ebizur said...

According to Table S6 of Yan et al. (2014), YCH251 (an M130+ Han from Hunan) is F3393+/F1370+. As per the current version of the ISOGG tree for Haplogroup C, this individual's genotype would place him in C1b -F1370, a clade which includes South Asian/Central Asian/Southwest Asian C1b1-M356 and Wallacean/Oceanian C1b2-M38.

So some sort of C1b-F1370 Y-DNA is found in China, too, and this clade is not limited to South Asia and Wallacea+Oceania.

Grey said...

"So some sort of C1b-F1370 Y-DNA is found in China, too"

If there was a C layer that was covered over (but not completely) by a D layer radiating out from a Himalayan interior source then you'd expect to find the most C on the periphery e.g. Japan, Korea, Oceania etc and in potential refuge regions in the core e.g. mountains and swamps (or regions that used to be swamps).

So I guess a test for the idea is if C in China tends to cluster in those kind of regions?

Chad Rohlfsen said...

http://www.science.ku.dk/english/press/news/2014/eske_indvandring_nabosex_2014/

Willerslev video

Matt said...

@ BO Ryk, also Native Americans are closer to K 14 than middle easterns are(excluding Caucasus). The order of his closest relatives seems to be in perfect correlation with ANE+WHG.

Well, the Middle Eastern samples fall into two classes - ones with heavy African admixture and one either without or lower levels, and the ones without are closer to Kostenki 14 (which is inherent in how the calculation works) at around a similar distance to Native Americans.
Still, K14 can't have much BE, as it the variation in its f3 is scarcely different from the rank order of ANE-WE ancestry as you say.

Probably less than the least BE contemporary Europeans... unless that BE was of a pretty divergent type, in which case it would be hard to calculate. If it had a lot of the BE we know about, that would inflate its similarity to other Europeans and deflate its similarity to Lithuanians.

If K14 has a lot of BE (which it may require if it is much further from East Eurasians than contemporary Europeans or Mesolithic Euros!), it seems like that BE would have to be at least as different from the BE in EEF and its West Eurasian component is as different from WHG (not that this is impossible given the ancient time).

John Smith said...

@Ebizur do you have the Yan et al paper?

---
It appears that possibly both y-dna F and C or associated with N mtdna leaving D to be associated with M. However if this is the case than people in East Asia and Oceanian and the Americas, and India should be closer to Africa than Scandinavia or Russia.

John Smith said...

I mean that someone in Chinese should be closer related to Africans than Russians are (If M is associated with D). Of course Chinese are closer to Russians than they are to Africans.

DDeden said...

"@ Grey @ DDeden
However, I think K14, if anything, solidifies support for multiple radiations from India/SEA, because K14 has Basal Eurasian even though it is on the Pontic-Caspian. This implies a route from the South and East, not so far west that lots of ancestry from the middle east comes into play. Also, look at the K14 morphology. " Ryukendo

I'm no geneticist, I might be all wrong; I use other data. IMO, K14 did not come from Wallacea/Papua/India, but some of his descendants went there after contact/admixture with Denisovans.

ryukendo kendow said...

@ Ebizur
Thanks for the info!

@ Davidski
I think the authors refer to MHGs as a european archaeological term (Mesolithic Hunter-gatherer), while WHG is a postulated ghost pop as defined by Laz.

Siberians, according to them, are best modeled as Even + Scandinavian MHG, which are really just a mix of WHG+ANE in laz's terms.

@ Tobus
For NAms apologies, I meant to say the reverse, as I did in later comments. That whole section was typed out very quickly.

About the oceanians thing, I was weirded out, because the full text contradicts what was stated in the Supplementary Materials. I quoted the full text because I did not want to reach conclusions from the supp that contradicted what the authors explicitly state.

The authors actually wrote, "We find that all contemporary non-Africans, except Australo-melanesians, are closer to either Mal'ta or MHGs than to K14." I was so confused when I read this and looked at the supp, because this implies the reverse for Oceanians, or at least an equidistant relationship for Oceanians, but the supp does not show that.

Is it the significance level?

@ Matt
Agree. However the D stats are more informative in this regard IMO.

Ajvide has higher f3 affinity with druze than Dai, but we know that Dai is closer to Ajvide than to Druze, and that info is lost when we get all our info from a single measure.

The fact that east asian are equi between stuttgart and K14 seems to imply something rather basal about K14, whether we want to concentrate this in a bit of his genome, making that very basal, or spread it over a chunk, making that as basal as that in Stuttgart.

@ DDeden
The autosome of K14 is closer to WHGs, implying that the pop he came from descended from another that gave rise to ANE, which in turn came from another pop that gave rise to ENA (Oceanian (ASI-Dai)). This is a sequential pattern of splits from the East, and the autosome is not subject to the same kind of information loss as haploid genetics is.

DDeden said...

Again, I'm not a geneticist.
But to clarify my comments: K-14 IMO was still in Don R. his near ancestors had continued eastward to meet Denisovans, and continued eastwards to Coast and then south to Phil, Borneo40ka & Papua, but a branch stayed in VietNam/Cambodia where a band found PhuQuoc Island which had a shrunken Tibetan wolf/aka PhuQuoc ridgeback dog, 34ka, which they used to pull their woven coracles/sleds, and were later overwhelmed by waves of proto-Austronesians. (may sound wacky but...)

Davidski said...

rk,

Loschbour and La Brana-1 are both unadmixed WHG.

Ebizur said...

John Smith wrote,

"do you have the Yan et al paper?"

The title is "Y Chromosomes of 40% Chinese Descend from Three Neolithic Super-Grandfathers." It is freely available at http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0105691.

ryukendo kendow said...

@ Davdiski
The paper states that the best results are Ajvide + Evens or Motala + Evens for Siberians, but uses the term MHG to refer to both La Brana/Loschour and Ajvide/Motala, who are a mix of WHG and ANE. That's why I think MHG is not so much a genetic term for them as much as a geographical one.

Davidski said...

Yes, I know, that's probably why they come to the erroneous conclusion in their model that present-day Siberians don't have any ANE ancestry.

Tobus said...

@ryukendo:
Yes, I think the significance level is too low for them to include Oceanians in the groups that are closer to MA-1/MHG's... I *don't* think they are saying the opposite though (at least if they are they're contradicting their own data). Some of the Papuan/Australian results are borderline significant, particularly the MA-1 results (closer than K14), but they're not as definite as the other pops and they seem to have just left them in the "too hard" basket rather than say anything explicit.

Chad Rohlfsen said...

David,
I don't think that they said there was no ANE in siberians. Scandinavian hunters were in MHG. Basically, it looks like they give everyone differing levels of what was WHG, BE, and ANE. It appears they have a clinal model with no mention of pure populations.

Davidski said...

In my opinion there should be a direct admixture edge running from the ANE node to the Yenisei node in the tree above.

Davidski said...

Here are three sets of PCA featuring Loschbour, MA-1 and Stuttgart (as a response to the comments in the other thread).

West Eurasia

https://drive.google.com/file/d/0B9o3EYTdM8lQbGJCR1VxeUg2X2M/view?usp=sharing

https://drive.google.com/file/d/0B9o3EYTdM8lQV1ZaVVdTSEMxTVU/view?usp=sharing

West Eurasia and Central Asia

https://drive.google.com/file/d/0B9o3EYTdM8lQd0RWRm53MTJpbEk/view?usp=sharing

https://drive.google.com/file/d/0B9o3EYTdM8lQV0RzeFZPU1djdWc/view?usp=sharing

Eurasia and the Americas

https://drive.google.com/file/d/0B9o3EYTdM8lQcTVxTDlEbVlnQjQ/view?usp=sharing

https://drive.google.com/file/d/0B9o3EYTdM8lQeW83NHROdzNLY2c/view?usp=sharing

ryukendo kendow said...

@ Davidski
Agree.

"..these results suggest that contemporary Siberian populations from the Yenisei basin derive part of their gene pool from a Eurasian HG population that shares ancestry with K14, but is more closely related to Scandinavian MHGs than to either MA1 or western European MHGs, indicating gene flow between their ancestors and Scandinavian Europe after K14 but prior to the Mesolithic (36.3 > x > 7 ka BP)."

They seem to have left out a lot of the things they conclude from the figures they drew.


@ Tobus
"Too hard" describes it well for Oceanians lol.

Chad Rohlfsen said...

David,
The PCA plot is giving mixed results. On the Central Asian one, equidistance from BE to WHG and ANE, causes some issues. If I use the equidistant thing, then Stuttgart and Sardinians are basically in the 8-10% range on the opposite side of the ANE line to Loschbour. If I use the line from BE to Stuttgart, then it is closer to WHG by a little bit, but Loschbour becomes shifted almost 20% of the way towards MA-1.

Chad Rohlfsen said...

Another issue with the line from Loschbour to Stuttgart, is that it makes even Palestians significantly ANE. It appears more than Northern Europeans.

BE being closer to Bedouins, on that equidistant thing, is the one that makes Loschbour very 'Eastern' shifted.

Chad Rohlfsen said...

Correction to that first post on the PCA.. The one that is near the Bedouins, is equidistant, not closer to WHG(if Loschbour is not full WHG), with that point being significantly 'West' of Lochbour.

terryt said...

"D) One B pop. in East Asia, inland, maybe up some mountains like say the Himalayas, close to surviving pre-humans pick up some useful genes from them that confers a significant advantage allowing them to expand outwards over-writing the C population in the majority of East Asia in a radius around the core source region".

To me that seems extremely likely. The origin and spread of the EDAR370A gene fits exactly that scenario. The authors of the relevant paper claim it formed in, or introgressed into, the modern human population around 37,000 years ago. A further commnet regarding your own one is that the 'significant advantage allowing them to expand outwards ' was most likely agriculture.

"this individual's genotype would place him in C1b -F1370"

Very interesting. So he's not part of the apparently widespread C1a Eurasian haplogroup.

"So some sort of C1b-F1370 Y-DNA is found in China, too, and this clade is not limited to South Asia and Wallacea+Oceania".

Which does rather support the idea that C1 and C2 split in China somewhere.

Chad Rohlfsen said...

Basically as close to equidistant and being close to the Stuttgart/Loschbour line will make Bedouins in the plot around 10%WHG, 15%ANE, 75%BE. Lezgins around 25%WHG, 30%ANE, 45%BE. Their small ENA contribution could be driving up the ANE and lowering WHG.

Grey said...

@terryt

"To me that seems extremely likely"

If it was (just guessing on my part) then if Asian D derived somehow from B + archaic (denisova) then it makes me wonder if African E came out of a similar process i.e. B + some other archaic?

Chad Rohlfsen said...

David,
Here is the game changer!

http://www.ebi.ac.uk/ena/data/view/PRJEB7618

I think Kostenki will show that your ANE k7 scores for the hunters are pretty true. I will post them next. Your PCA plot is about spot on.

Seinundzeit said...

Very interesting PCA plots.

If my understanding of the West Eurasia/Central Asia PCA plot isn't totally off the mark, the closest population to MA1 (when accounting for any shift towards Loschbour on eigenvector 2) are the Kalash. On a "regional" level, the closest populations to MA1 are Central/South Asians (again, accounting for any shift towards Loschbour on eigenvector 2). But that's expected, given the results we've seen for the Eurogenes K7 test (both the actual ADMIXTURE run, and the DIY calculator).

The closest populations to Loschbour seem to be Lithuanians+Estonians (not surprising at all), and the closest population to Stuttgart are Sardinians (plainly obvious). All in all, the West Eurasia/Central Asia plot is very reasonable.

Just a side note, but I think this PCA plot is an additional piece of evidence for claiming that Pamiri Tajiks have a good amount of WHG admixture (by Central/South Asian standards). Since WHG is quite weak in this region, the Pamiri Tajiks probably have less WHG in comparison to Lezgins and Chechens, but they'll definitely exceed other populations in South Central Asia. This was evident in the f3 stats David shared with us, as the Pamiri Tajiks often scored Burusho+Loschbour, Kalash+Loschbour, and Pashtun+Loscbour (or these same populations+La Brana-1). By contrast, they never scored anything involving other Central Asian populations+MA1, so their ANE levels are likely to be average for the region (something between 30%-40%, like most South Central Asians).

The Pamiri Tajiks are a very interesting population. Like Pashtuns, they speak languages linked to those spoken by "Scythians" on the eastern steppe (basically, like Pashtuns, they can claim some historical/cultural connection to "Scythians", whatever that amorphous category is supposed to designate). If that aspect of their genetic ancestry has been preserved to a greater extent (in comparison to Pashtuns), this opens up the possibility that there was substantial WHG ancestry on the eastern steppe.

Chad Rohlfsen said...

David,
Just for the hell of it. Here are some numbers. The funny thing, is that the PCA plots kind of replicate this. If I remember correctly, Motala was about 35% of the way to MA-1. The Willerslev group does have Ajv58 below Motala, which they would be in your plot as well, by these numbers. The distances on Willerslev-Sikora are about those too.

Loschbour
ANE 7.35%
ASE 0.49%
WHG-UHG 88.70%
East_Eurasian 3.09%
West_African -
East_African 0.36%
ENF -

La Brana
ANE 3.98%
ASE 0.45%
WHG-UHG 92.37%
East_Eurasian 2.31%
West_African 0.86%
East_African -
ENF -

KO1
ANE 6.55%
ASE -
WHG-UHG 93.07%
East_Eurasian 0.15%
West_African -
East_African 0.22%
ENF -

Ajv58
ANE 14.54%
ASE 2.06%
WHG-UHG 78.38%
East_Eurasian 2.21%
West_African 0.49%
East_African 2.32%
ENF -

Motala12
ANE 19.62%
ASE -
WHG-UHG 80.23%
East_Eurasian 0.14%
West_African -
East_African -
ENF -

MA-1
ANE 49.08%
ASE 11.22%
WHG-UHG 33.58%
East_Eurasian 1.54%
West_African -
East_African 4.58%
ENF -



Chad Rohlfsen said...

MA-1 was shift South from the line going from Loschbour to Motala, as well.

Chad Rohlfsen said...

I could be wrong. I wouldn't doubt it, but these numbers are strikingly similar to some plots.

David,
Did you see my post about the Kostenki genome?

Colin Welling said...

from the paper the yenisei are closer to SHG than WHG or MA, which explains why the yenisei are linked directly to MHG (WHG+SHG). Its not hard to imagine gene flow from scandinavia to the yenisei area by a norther route that mostly misses descendants closely related to MA.

Davidski said...

But it's even easier to imagine that the Yenisei Siberians have ANE ancestry from Siberia plus some WHG/ANE from Eastern Europe or nearby.

This might indeed look a lot like SHG ancestry, but if so, then there's no need to postulate a population movement from Scandinavia to Siberia.

terryt said...

"if Asian D derived somehow from B + archaic (denisova) then it makes me wonder if African E came out of a similar process i.e. B + some other archaic?"

Another thing that 'I think' is that we have only just scratched the surface of archaic admixture. I'm sure we will discover more than just Neanderthal and Denisova. Mind you haplogroups do not change through hybridisation. And D and E apparently have a common source, as far as we know.

Ebizur said...

terryt wrote,

"Very interesting. So he's not part of the apparently widespread C1a Eurasian haplogroup."

C1b-F1370 is very widespread, from Arabia to Rapa Nui. I just want people to know that it is also found in China.

C1a is actually rarer and more limited in its distribution (only about 5% in Japan and trace amounts in Europe) than C1b at present.

Grey said,

"If it was (just guessing on my part) then if Asian D derived somehow from B + archaic (denisova) then it makes me wonder if African E came out of a similar process i.e. B + some other archaic?"

Japanese and continental East/Central Asian D actually form a clade separate from that to which the rare Filipino D2 belongs. Andamanese D might fall on the D2 side of the split, but this has not been confirmed yet.

In any case, Japanese and continental Asian D are not so old as many people have assumed them to be. When compared under the same parameters and ignoring Filipino D2 (for which I do not possess any data from which to infer a TMRCA with D1), C ({C1 + C2}) is the oldest Y-DNA lineage in East Asia. D1-CTS11577 (now found mainly among Japanese, Tibetans, Qiangs, Turks, and Mongols, but also with very low frequency in some unexpected places, such as Shandong) appears to be significantly (approx. 15,000 years) younger than C, with a TMRCA only about the same as that of NO-M214. Of course, since C1-F3393 Y-DNA has been found in the Kostenki 14 specimen from eastern Europe, with an earlier Siberian (Ust-Ishim) belonging to pre-NO and a later Siberian (Malta) belonging to pre-R, the assumption based on modern distribution that the MRCA of C1 and C2 has lived in eastern Asia may need to be revised. C1 and C2 may have split somewhere in western Eurasia and later migrated separately to eastern Asia (and thence to Oceania in the case of C1 and America in the case of C2).

Yunnanese/Lolo-Burmese F2-M427/M428 has a great TMRCA with G-M201 (only about 7000 years less than the TMRCA of C1 and C2, or about 8000 years greater than the TMRCA of all extant D1), but the MRCA of all extant F2-M427/M428 appears to be very recent (like 4000 to 5000 YBP), so it is difficult to tell when or how this clade has arrived in Yunnan.

Davidski wrote,

"But it's even easier to imagine that the Yenisei Siberians have ANE ancestry from Siberia plus some WHG/ANE from Eastern Europe or nearby.

This might indeed look a lot like SHG ancestry, but if so, then there's no need to postulate a population movement from Scandinavia to Siberia."

What about the finding that the mtDNA of modern populations in western Siberia (even some populations as far to the southeast as the Altai-Sayan region) is similar to the mtDNA of Mesolithic people in Karelia? Please note that the Kamasins and Mators lived in the Altai-Sayan region and spoke Uralic (Samoyedic) languages as recently as the 19th century. Yeniseian (Ket-related) toponyms also occur in that region. On what grounds would you reject a hypothesis that this Samoyedic/Yeniseian mix (or only one or the other constituent element of it) has migrated eastward from an earlier home in the vicinity of Karelia?

ryukendo kendow said...

@ Ebizur @ Davidski
It is quite apparent that Uralic has its ultimate origins further east, and Uralic and Altaic represent two waves of East-Asian-like populations entering into Siberia, carrying Hgs N and C respectively. Uralic first, Altaic later.

Below these, Yeniseian might be the oldest wave, a remnant of the same wave of East-Asian-like people who mixed with ANE to form the pops in the Americas; esp as Edward Vadja's theory of Dene-Yeniseian has gained widspreade credence. This might be represented via the Hg Q still scattered across Siberia.

The fact that NAms, the earliest wave, have no WHG, only ANE, while Kets and later Uralic pops do, might mean that WHG ancestry steadily increased over time in the Taiga, such that before the Uralics and Altaics entered Siberia an ANE-WHG mix was present deep into the East.

We can get a timing for this, because AG-2 is similar to MA-1 in being pure ANE (as far as we know), and AG2 is dated to 17 kya.

The order of colonisation would be 1) ANE, 2) 1st ENA migration ---> NAms, 3) WHG seeping into the Taiga, 4) 2nd ENA migration ---> Uralics, 5) 3rd ENA migration ---> Altaics.

Davidski said...

Karelia is in Eastern Europe, not Scandinavia, so if there's Karelian admixture in Siberia then that supports my argument.

Anyway, full mtDNA sequences show that West Eurasian ancestry in Siberia has two main sources: Eastern Europe and West Asia. Scandinavia is not an option.

http://www.biomedcentral.com/1471-2148/14/217

Davidski said...

Chad, yes, I sent the Kostenki14 link to Felix yesterday.

I'm looking forward to seeing the K15 result for this genome.

Ebizur said...

r.k. wrote,

"It is quite apparent that Uralic has its ultimate origins further east, and Uralic and Altaic represent two waves of East-Asian-like populations entering into Siberia, carrying Hgs N and C respectively. Uralic first, Altaic later."

I don't mean to sound rude, but that is an assertion, and not an argument.

Why is the mtDNA pool of Mesolithic people in Karelia most similar to the mtDNA of modern pre-Slavic people (including Uralic speakers) in western Siberia, but the mtDNA of modern Uralic (Finnic) speakers in Karelia almost the same as that of nearby Indo-European and other Finnic speakers? In other words:

Pop. 1) Modern Karelians: Uralic (Finnic) speakers, mtDNA roughly same as that of nearby Indo-European and other Finnic speakers

Pop. 2) Mesolithic people in Karelia: linguistic affiliation unknown, mtDNA pool is similar to that of modern speakers of Uralic, Yeniseian, etc. in Western Siberia

Pop. 3) Modern "aborigines" of Western Siberia: speak Uralic (Samoyedic & Ob-Ugric) or Yeniseian languages (some other non-Slavic populations in the region speak Tungusic, Turkic, or Mongolic languages, but they are generally believed to be more recent in the region than Uralic- or Yeniseian-speaking populations), mtDNA pool is similar to that of Mesolithic inhabitants of Karelia

If you want the Asian-leaning mtDNA profile of modern Western Siberians and Mesolithic people in Karelia to be a signal of Uralic origin in eastern Asia, then you have to explain the transition from a similar mtDNA profile in Mesolithic inhabitants of Karelia to a much more European-leaning mtDNA profile in modern inhabitants of Karelia despite the latter group's speaking a Uralic language. (The Mesolithic inhabitants of Karelia may have spoken a language related to Uralic, or they may have spoken some other language entirely; this simply cannot be known.) Would you posit that expanding Indo-Europeans first conquered the territory of Karelia from the descendants of the Mesolithic inhabitants, replacing the gene pool almost completely, only to be later conquered by some Finnic-speaking group who did not introduce much Asian-affiliated mtDNA?

Who do you propose has introduced all that WHG-affiliated autosomal DNA into Western Siberia? If you assume that Yeniseian is associated with ENA+ANE because of the hypothesized relationship with Na-Dene of North America (and presumed lack of WHG affinity in pre-Columbian Na-Dene speakers) and you assume that Uralic is associated with another layer of ENA, then what language do you suppose the WHG people "seeping into the Taiga" might have spoken?

Eduardo Pinto said...

Some results from Felix's preliminary autosomal file of K14.
This file is lacking too many SNPs

5.59% ANE
11.42% ASE
47.76% WHG-UHG
0.02% East_Eurasian
3.35% West_African
18.85% East_African
13.01% ENF

0.56% ANE
0.16% ASE
39.28% WHG-UHG
0.00% East_Eurasian
0.89% West_African
18.52% East_African
21.11% ENF
19.49% Oceanian

Dienekes' globe13

0.00% Siberian
0.00% Amerindian
0.35% West_African
19.32% Palaeo_African
13.05% Southwest_Asian
0.00% East_Asian
10.87% Mediterranean
21.13% Australasian
0.54% Arctic
0.00% West_Asian
30.52% North_European
4.22% South_Asian
0.00% East_African



Davidski said...

Where is this preliminary file?

Eduardo Pinto said...

https://drive.google.com/folderview?id=0B49499_WVp2fZ0VmZ0duSHEyMjQ&usp=sharing&tid=0B49499_WVp2fQ1hDQVJJVzhRNzg#list

I used Complete_Autosomal.csv.gz

Ebizur said...

Davidski wrote,

"Karelia is in Eastern Europe, not Scandinavia, so if there's Karelian admixture in Siberia then that supports my argument.

Anyway, full mtDNA sequences show that West Eurasian ancestry in Siberia has two main sources: Eastern Europe and West Asia. Scandinavia is not an option."

Karelia is adjacent to Finland and located between Scandinavia and Western Siberia.

We know that certain Mesolithic inhabitants of Karelia have an mtDNA pool that is similar to that of modern non-Slavic inhabitants of Western Siberia. Is any information regarding the mtDNA of Western Siberian contemporaries of the Mesolithic Karelians available?

Davidski said...

Ebizur,

No, I don't know of any pre-Andronovo aDNA from Siberia apart from MA-1 and AG-2.

Eduardo,

Thanks. There's another nine of those runs to go before we get the full autosomal file, so those results will probably change quite a bit.

ryukendo kendow said...

@ Ebizur
Well, you're not being rude, those are reasonable objections. I don't think we can know what those populations spoke, because Mesolithic is too old.

For the Uralic languages, I'm basing my observation off of Janhunen's and Sammallahti's arguments about the matter, as well as the fact that 1) the component associated with Uralic peaks in Nganassan, a mixed East-West population, and declines westwards, not in a West Eurasian population declining eastwards, 2) there is quite clear evidence of pre-Uralic substrates in the Uralics in Scandinavia, and some have even proposed uralisation after IE-isation; and 3) Uralic seems to have a great deal of contacts with Yukhaghir.

Secondly, the Y-DNA evidence, esp N, points to movements in the opposite direction from East Asia, and languages are known to be inherited more strongly if the incoming elite are male-biased. The connection between N and Uralic has been made many times before.

It just seems to me that WHG seeping into Siberia occurred prior to East Asian contributions to the region, and that the Karelian-like mtDNA there should be associated with something much older. Uralic dating by linguistic methods typically find an age of 5kya or so only.

In any case I'm glad to hear your thoughts on the matter.

Balaji said...

Now that we have had some time to digest these findings, perhaps they are not so surprising after all. From Ust Ishim, we knew that Middle Eastern populations had already diverged from other non-Africans 45,000 years ago. The populations of the Caucasus have a high amount of this AME By 38.000 years ago, this population must have reached the Northern Caucasus and interacted with WHG populations in Southern Russia to produce K14. This would have been a case of diffusion of Middle Eastern genes into a European population from their point of contact. However the amount of Middle Eastern genes would have fallen quickly with increasing distance from the Northern Caucasus and thus must have had only a local effect. Unlike this, the Neolithic demic expansion brought Middle Eastern genes to all of Europe,

Balaji said...

I share Hector's skepticism about the branching model that the authors have proposed.

I have evidence that ANE does form a clade with ENA to the exclusion of WHG. Consider the following f3 statistics which I got from Davidski’s Eurogenes Blog.

http://eurogenes.blogspot.com/2014/07/f3-stats-100-present-day-populations.html

f3(Assyrian;Dai,Sardinian) -0.00059462 0.000194433 -3.05822

From Lazaridis, we know that Sardinians are 0.82 EEF, 0.18 WHG and 0.01 ANE. Lazaridis does not give information about Assyrians but Assyrians as a Middle Eastern population have 0 “excess” WHG. They are sure to have more of the BEA than the Sardinians. who have 0.82*0.44=0.36. A reasonable guess for BEA for Assyrians is 0.6 with ANE of 0.15 and a WHG-like “UHG” of 0.25. The above f3 statistic is negative, not because Assyrians have East Asian admixture. The Dai are standing-in for ANE. The statistic is negative even though Sardinians have UHG+WHG+ANE=0.64 whereas Assyrians have UHG+WHG+ANE=0.4. The extra ANE that Assyrians have makes them appear to be a mixture of Sardinians and Dai.

ryukendo kendow said...

@ Balaji
What other Middle East populations with ANE share this pattern?

Davidski said...

There might be low level ASI admixture across the Near East. See here...

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0073682

If so, the Dai would be a good proxy for it.

Kristiina said...

Ebizur, this is Jaska’s well justified opinion on this Uralic matter:
The deepest taxonomic gap (between Finno-Permic and Ugro-Samoyedic) was located in Europe. That is one hint towards the area of dispersion of Late Proto-Uralic in Europe, but of course not the only one. We cannot speculate with some hypothetical, lost Uralic languages, so we have to play with the survived languages only.
So far there is no single Y-chromosomal haplogroup which would be common in every Uralic branch. N1c1 is common elsewhere in the family (2 out of 4 ancient Hungarian nobility samples were N1c1), but N1b is the only haplogroup shared by all the Samoyedic peoples.
We must remember that languages did not spread to their present areas at once, but along many consequent steps. For example Tundra Nenets spoken north of the Volga-Kama region (he original homeland of Late Proto-Uralic) did not spread right there, but in several steps:
1. From Volga-Kama to the east to Sayan Mountains (Pre-Proto-Samoyedic)
2. From Sayan Mountains to the north between Yenisei and Ob (Proto-North-Samoyedic)
3. From Lower Yenisei Valley to the west (Proto-Nenets)
4. From Lower Ob to the west (Tundra Nenets)

All these linguistic stages can be connected to different composition of haplogroups. That is the reason why we cannot any more trace which haplogroup spread the Proto-Uralic language.

We cannot guess the linguistic homeland on the basis of haplogroups, but just the opposite: we must find the linguistic homeland on the basis of linguistic evidence, and only after that we can look if any survived haplogroup matches our result. It is a possibility that the haplogroup which spread the Proto-Uralic language has since then disappeared.
We know that Late Proto-Uralic was spoken in Europe, but its ancestor language seems to have been spoken in Siberia.

As for ancient Siberian mtDNA, this paper is highly informative: http://dienekes.blogspot.fi/2012/07/population-strata-in-west-siberian.html
http://www.degruyter.com/view/books/9783110266306/9783110266306.93/9783110266306.93.xml.

As for modern yDNA:
Northern Selkups:
Q1a3-(xL330) 66.4%, R1a1 – 19%, N1b - 6.9%, R1b - 6.1%, C - 1.5%,
Mansi:
N1c - 16%, R1a1 - 6%, N1b 6%, R1b 2%, I - 4% (here something is missing! – according to my papers it should be
N1c - 16%, R1a1 - 8%, N1b - 60%, R1b - 4%, I - 8%, J- 4%)
Khanty
N1b - 48%, N1c1 - 38%, R1a1 - 7%, Q-L330 - 1%, G - 1%
Northern Khanty
N1b - 57%, Q-L330 - 21%, R1a1 - 21%, N1c1 - 7%, R1b1b2 - 0.9%
Kets:
Q-L330 - 84%, N1c - 8%, N1b - 4%, R1a - 4%

According to that Tomsky paper, R1b of southern Selkups is M73, so that goes probably also for Northern Selkups.

Grey said...

@Balaji

"However the amount of Middle Eastern genes would have fallen quickly with increasing distance from the Northern Caucasus..."

Isn't that the question though - how much of this layer of dna was already in Europe before the neolithic expansion as part of WHG?

It doesn't even need to be a lot in total. If it was clustered among certain euro pops. then might it not skew that particular group's WHG/EEF percentages?

In particular I'd wonder about the EEF estimates among those Baltic populations with the most WHG or maybe mountain populations - also those inland Sardinians.

Kristiina said...

This is my recent personal opinion on this matter: the proto-Uralic constructions rely heavily on shared words between Saami, Samoyedic and Finnish languages, so it is possible that the Uralic protolanguage as it is constructed at the moment is more related to the language of ancient northeners, such as ancient Karelians of Yuzhnyy Oleni Ostrov (7,500 uncal yBP, linked with Siberian Butovo microblade culture), whatever their y DNA was, than to Volga-Finnic groups. However, with this I do not want to call into question the unity of Uralic language family and the existance of that cultural area.

Grey said...

A thought regarding Finns, Siberia etc.

Premise:
Non-migratory gene flow mostly involves bride swapping between adjacent groups.

The effect of bride-swapping on gene flow is proportional to the number of groups in the chain from A to B.

The number of groups is the total distance divided by the size of each group's territory.

The physical distance between two points on the same longitude is lower the further north you go.

Then east-west gene flow by bride swapping would be higher the further north you went (if all else was equal) so in that case it might turn out that Baltic->Mongol gene flow was faster going:

north -> east -> south

rather than directly east

(and vice versa)

(this would only apply to maternal dna of course)


Grey said...

@terryt

"we have only just scratched the surface of archaic admixture. I'm sure we will discover more than just Neanderthal and Denisova."

Yes, I'm thinking that.

"Mind you haplogroups do not change through hybridisation."

Ah, that sounds like my next google project then.

John Smith said...

@ Kristiina

The R1b in Siberia is probably Q.
See http://www.nature.com/nature/journal/v466/n7303/extref/nature09103-s1.pdf and find how all of the R1b-M73 in the Hazara was proven to not belong to R1.
In a other study these samples belonged to R1b-m73 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1380230/.
See http://snag.gy/wCfoa.jpg.

Colin Welling said...

[i]The R1b in Siberia is probably Q.[/i]

I have yet to hear someone with a good amount of knowledge on ydna challenge the r1b findings in the Bashkirs or Siberia.

There are multiple studies showing r1b in Siberia with similar results. Why do you think they all share the same flaw?

John Smith said...

@Colin Welling

Did you read my sources?

All I know is that Behar relabeled Sengupta's R1b-m73 as not a type of R1.

Colin Welling said...

Does anybody know how well of a fit la brana is for WHG/MHG? Both this paper and the Laz paper say that brana has no ANE or Basel Eurasian and is just WHG/MHG. But I remember bloggers doing analysis on la brana showed that la brana has some type of southern ancestry. Its likely to just be noise but would if la brana shares some very basel eurasian which is similar to the one in k14 but somehow these studies missed that. any ideas or reason to reject this notion?

Chad Rohlfsen said...

There is r1b l23 spread as far as Mongolia. Bashkirs are a mix of m269 and m73.

Colin Welling said...

but how about the reported m73 in the bashkirs and siberians? do we know for a fact that they are solid?

Colin Welling said...

btw, it seems that a study as recent as 2013 is finding r1b-m73 in siberia. DiCristofaro et al. 2013

ryukendo kendow said...

@ Kristiina @ Ebizur
I wholly agree. While late Proto-Uralic appears to be spoken just West of the Urals, pre-proto Uralic was placed as far east as the altai-saiyan by Haakkinen, to explain yukhaghir connections at the proto language level, and very strong typological similarities with altaic, which more or less demand the existence of an areal effect at an early point in both their histories.

@ Balaji
Found the spreadsheet.
The pattern of negative f3(X; Dai,Sardinian) seems to be quite widespread in the middle east...

@ Davidski
Is there a way to map these f3 figures? Could you pull the negative (Dai, Sardinian) into a spreadsheet on its own?

Thanks!

Hector said...

If you examine K14's Y-SNPs you will see a lot of false positives. If these were on anywhere else other than NRY they would have given false affinity to various West Eurasian populations.

We will just have to wait until abler researchers like Paabo reanalyze this sample.

Most of the arguments here are of hair-splitting nature. Since this sample appears to be contaminated(or beset by lab errors) your "arguments" are comical at best.

And by the way... a lot of your "pain" will be gone once you abandon the simplistic model of ANE and WHG being sister branches.

I reckon a lot of you are Asatru folks. That is pseudo science much like the one practiced by Polako.

Roy King said...

@John Smith
That is ridiculous---I was present when Peter Underhill genotyped the Hazara who are definitely M73 and definitely R1b---P297 splits into M269 and M73. And, yes, the Bashkirs, Karachays and Balkars have a relatively high frequency of M73.

@Davidski
Are you able to run K14--Kostenki through your admixture programs now that Felix has processed the raw data?

Davidski said...

It looks like Felix has another four runs to go. He should be done within a day or so, and then I'll be able to run the file.

Davidski said...

Balaji and rk,


I've run various D-stats to see if MA-1 and the Dai form a clade, like D(Chimp,Yoruba; MA-1, Dai), and they don't, because I'm seeing significant deviations from zero in all of the tests. So unless I'm doing something wrong, they're not a clade.

By the way, here are those f3-stats involving the Sardinians and Dai. The latter obviously aren't a good proxy for MA-1 in this type of a test.

https://docs.google.com/spreadsheets/d/1cvE90eTpVAYpnbmuHJT2X3-xbBizLL3uRYdKtnhXFz0/edit?usp=sharing

CW,

Loschbour and La Brana-1 do form a clade. What this suggests is that if La Brana-1 has some Basal Eurasian ancestry then it's very low.

Matt said...

@ Davidski, thanks for those PCA.
PC3 on the West Eurasia plot does seem to place West Asia and Southwest Europe closer together, as expected (although everyone modern is quite compressed on this axis), but contrasts them to MA1. Surprising, not sure what, if anything that means.

PC4 also shows an additional level of similarity / dissimiliarity where all West Eurasians are alike and equally unlike to MA-1.

Either way seems like both these PC are dominated by some more differentiation from MA1 that is unrelated to the pattern in PC2 for some reason.

Chad, with the PCA, I wouldn't worry too much about trying to find an equidistant point from Losch and MA1 - these dimensions 1 and 2 don't necessarily scale equally or represent total genetic distance. Just look at the intersections is probably the best we can do.

Davidski: "But it's even easier to imagine that the Yenisei Siberians have ANE ancestry from Siberia plus some WHG/ANE from Eastern Europe or nearby.

This might indeed look a lot like SHG ancestry, but if so, then there's no need to postulate a population movement from Scandinavia to Siberia."


Agreed, I think for sure that the
ancestry came from Eastern Europe, as it is close and huge while Scandinavia is small and far away - even across the relatively short distances along the north, (although these are, like I say relatively short). And it is a little cackhanded in their presented tree model to elide that SHG like Motala seem to model as a ANE+WHG group (or as an intermediately branching population, either way).

But I think it might be telling for us about how much WHG and ENA "unadmixed" ANE ancestry would be present in North Eurasia by the era when Yenisians were formed, if the ancestry in Yenisians is closer to the 20% ANE, 80% WHG modelled SHG rather than the 100% ANE MA1. The midpoint between SHG and ANE would be 60% ANE, 40% WHG, so this would indicate that the mixing population into Yenisians was like 50% ANE, 50% WHG. And this should be deep into Russia.

...

On these models generally, while I obviously don't agree with fairly absurd claims that they relate to "Eurocentricism", it does seem that K14 necessitates us to add an additional kind of Basal Eurasian (BE2) which is divergent from the Basal Eurasian in Stuttgart (BE1).

Otherwise, how can we satisfy that K14 is equally distant to non-Africans as Stuttgart (who let's remember is *further* from East non-Africans than present day Europeans generally are) while the closest relative to K14 is the Lithuanians and not Stuttgart or Middle Eastern people? Stuttgart is modelled as 44% BE.

So, it seems you need two BE components who are substantially divergent compared to one another compared to K14 and Lithuanians West Eurasia clade ancestry. If BE in Stuttgart and K14 were similar, then it would seem like other populations than LTU would be closer to K14.

It depends on a lot of statistical comparisons, so I am not 100% but it seems some form of ghost in the Middle East, that mixed with WHG to give rise to EEF, probably will not go away, and is real (because of the tree modelling in Lazaridis).

At the same time, if we need two divergent BE ghosts, is it not simpler to just model Basal East Eurasian ancestry into a common ancestor of WHG and ANE, rather than add another ghost? And this is very early into Upper Paleolithic differentiation into different physical anthropology forms, back when people in Eurasia seem more or less to be generic Upper Paleolithic people with unusual forms compared to modern day people (and are more alike to one another than any is to any present day person), so there are no major phys anth aberations caused by this.

Basal East Eurasian ancestry into a WHG-ANE clade was rejected in Lazaridis as not parsimonious, compared to a single Basal Eurasian population. Is this still the case if it looks like we have to have 2 divergent Basal Eurasian populations? It's something I'm unsure about.

ryukendo kendow said...

@Davidski
Thanks!

I always thought the ane whg node was quite solid. There's just too much to explain otherwise, not least the fact that ane is no closer to ENA than whg is, while it is much closer to whg than ENA is.

If there was asi in the middle east could we quantify it?

@Matt
"Otherwise, how can we satisfy that K14 is equally distant to non-Africans as Stuttgart (who let's remember is *further* from East non-Africans than present day Europeans generally are) while the closest relative to K14 is the Lithuanians and not Stuttgart or Middle Eastern people? Stuttgart is modelled as 44% BE. "

I'm not sure f3 s can be compared with d stats in an informative way. Ajvide is closer by 'affinity' f3 to druze than to dai, but the more important measure is that dai is closer to ajvide than to druze by d stats; same with all ENA pops + mal'ta.

I do however agree that the small portion of basal in k14 is not properly resolved. All that was proposed was an outgroup to crown eurasian, but if course there could've been many. It's attribution to 'basal' in laz's terms by the authors was merely postulated through ADMIXTURE scoring in a near east like component, but this is not a formal measure. I think f3 "admixture" stats with all pops in the eurogenes dataset would be extremely interesting once the genome is out, esp as k14 scores non trivial African at every k.

Last thing: if there was a basal-2 component it would help to explain the melanesian exception, if it contributed to K14 and oceaneans but not Stuttgart or any other eurasian pop, (but this sounds to me unlikely on geographical grounds...) The other possibility is that there was gene flow between a subgroup of basal that contributed to stuttgart and all members of crown eurasian, but this did not reach oceanians and the subgroup of basal in k14.

Chad Rohlfsen said...

How informative might a PCA of just ancient samples be? Something with Loschbour, La Brana, KO1, Motala, Ajv58, MA-1, Stuttgart, CO1, BR1,BR2, and IR1.

Davidski said...

The ASI in the Near East is mostly cryptic, probably because it's much older than the Gypsy migrations and other historic events, so it's hard to estimate accurately. Here's something of an attempt from Laz et al.

https://drive.google.com/file/d/0B9o3EYTdM8lQOTRMSzkwRzlVZzg/view?usp=sharing

Davidski said...

Chad, all of the ancient samples on the PCA would have to be of a comparable quality (preferably high coverage). So it's probably not a useful exercise until we get more 10x and above genomes, plus a high quality ANE genome.

Krefter said...

Anyone know what's up with GEDmatch? It loads for eternity in admixture runs(doesn't give results), while earlier today it was working find.

Chad Rohlfsen said...

Okay. Thanks!

Davidski said...

It's interesting that in this study K14 and La Brana-1 are shown to have elevated levels of Neanderthal ancestry, and they both score Sub-Saharan admixture in some tests. In fact, K14 shows the Mbuti type of SSA admix, which suggests that it's indeed something archaic.

Grey said...

I can't remember where it was from now - I think some of Dionekes' tests - but I seem to recall odd African components showing up in some of the Baltic pops. that was put down to noise but made me wonder if there was an old layer underneath that survived better in refuge regions (and I assume wetlands make good defensive terrain for the aquatic locals) e.g. a layer that was < 1% on non refuge terrain and maybe c. 2% in refuge terrain or something like that.

ryukendo kendow said...

@ Davidski

Thats an extremely interesting suggestion which might go some way in explaining some phenomena, incl. why 1) Oceanians, who likely have the highest level of Archaic in any pop, are closer to K14 than other pops in K14 vs Stuttgart comparison 2) Sub Saharan Africans are, conversely, closer to MA-1/Loschour than to k14.

Perhaps ADMIXTURE dumps the 'excess' variation caused by archaic introgression into the African bucket, because this introgression will pull in a relatively nonspecific direction, not shifting K14 towards any population really, so ADMIXTURE dumps it in the largest container it can find.

Thanks very much for that (Karitiana, Onge) table.

On another note, it seems to me that they could use that same method to put a lower bound on ANE in Yamnaya and Karelian though. An estimate for Basal will not be affected by ENA, so it seems to me a calc for Basal + this stat here could circumvent the ENA/ANE mixup problem...?

Seinundzeit said...

rk,

If a sample/population has ENA admixture, that formula underestimates ANE admixture (the formula used for estimating a lower bound for ANE admixture in Near Eastern populations). For example, according to this formula, the lower bound for my ANE admixture is 27%. But for a Punjabi friend whose raw-data we had, 23%. This just can't be correct, Punjabis and Pashtuns probably have approximately equal amounts of ANE admixture (around 35%). My ENA admixture brings me down to Lezgin/Chechen levels (they also scored 27%, back when we tried this), and it brings my Punjabi friend down to south Caucasian levels. This equation gives a Tamil Brahmin individual exactly 0% ANE, even though they are probably around 30% ANE admixed.

ryukendo kendow said...

@ Sein
Thanks for the explanation.
I had thought that the discrepancy between the fitted ANE and the lower bound could be attributed with some certainty wholly to ENA. It seems like there is indeed no way to disentangle the two.

@ Chad
Since you have had some good approximations using measuring of distances on PCAs, we could have a repeated procedure where only stuttgart, loschour, bedouin, MA-1 and Dai are included as 'references' in a plot, with a single test population or a series of closely related test pops, e.g. all from central asia. After a bit of calibration wrt some test populations for whom percentages are known, e.g lazaridi's estimates for Europe and Karitiana, perhaps we can use this to get a series of very rough estimates for pops like Yamnaya or Karelian when they do come out.

I think we might have to use 3 eigenvectors to get good results. Or we could have one PCA with WHG+Basal+ENA references, and another with WHG+Basal+MA-1, and a third with WHG+ANE+ENA, if we do not want 'cross-contamination' of components with each other.

What do you think?

Kristiina said...

”Davidski: "But it's even easier to imagine that the Yenisei Siberians have ANE ancestry from Siberia plus some WHG/ANE from Eastern Europe or nearby.”

”This might indeed look a lot like SHG ancestry, but if so, then there's no need to postulate a population movement from Scandinavia to Siberia."

YDNA Q-L330 of the Yeniseian Kets must have moved from east to west (Q-L330 is also found in South Siberia and Yeniseian languages have eastern, even Beringian, correspondencies. Moreover, unlike Nenets and Nganasans, Kets also have traces of Beringian Arctic ancestry and Turkic ancestry. When you look at level 10 of this admixture chart http://biorxiv.org/content/biorxiv/suppl/2014/07/30/005850.DC1/005850-1.pdf, you see that the Yeniseian western Eurasian anvestry is Volga-Uralic like and not Russian like. On the other hand, we know that there has been a west to east movement of Uralic groups: (linguistic ancestors of) Nenets ended up from Kama area to the Central Siberian Tundra, (linguistic ancestors of) Hanti and Mansi moved from west of the Urals to the east of the Urals and Komi Zyrians moved from south to north.

I think that it is obvious that Yeniseians mixed with Uralic goups and got their WHG from them.

Balaji said...

Davidski and Ryukendo,

Here are four European f3 values.

Greek;Dai,French_Basque -0.000365561 0.000151607 -2.41124
Spanish;Dai,French_Basque -0.000975007 0.000124464 -7.83365
East_Sicilian;Dai,French_Basque -0.000569748 0.000184245 -3.09234
Tuscan;Dai,French_Basque -0.000432676 0.000151683 -2.8525

I chose these particular populations because according to Lazaridis, Basques have 0.59 EEF which is less than the EEF of Sicilians (.9), Greeks (0.79), Spanish (0.81) and Tuscans (0.75).

The Dai can only be filling-in for ANE implying that ANE and ENA form a clade to the exclusion of WHG.

Balaji said...

Davidski,

Regarding the PLOS paper that you referred to, it is very likely that the remains from which they extracted ASI ancient DNA are from merchants who had come from India and not from any large-scale migration.

However since the time of the Islamic Slave trade, Africans, Indians and others have been transported to the Middle East and contributed to the gene pool there. See the following paper for example.

http://www.biomedcentral.com/content/pdf/1471-2148-11-288.pdf

The Assyrians are Christians and would not have been affected by gene flow from the Islamic slave trade and neither would any of the following populations.

Ashkenazi;Dai,Sardinian -0.000297346 0.000155065 -1.91756
Armenian;Dai,Sardinian -0.000435056 0.000143102 -3.04019
Cyprian;Dai,Sardinian -0.000721083 0.000160358 -4.49671
East_Sicilian;Dai,Sardinian -0.00168635 0.000173865 -9.69919

Davidski said...

Nope, MA-1 and Dai are not a clade relative to Loschbour. There are different ways to set up these tests, but it's pretty obvious that these two are not a clade, while Loschbour and La Brana-1 do look like a clade.

Chimp Loschbour : Dai MA-1 0.0504 7.792

Chimp MA-1 : Loschbour La_Brana-1 -0.0060 -0.736

ryukendo kendow said...

@ Balaji

Thanks for bringing attention to those numbers, which are intriguing.

I think tests of MA-1 itself show us quite directly its proximity to WHG and distance from Dai. Also, the more ancestry NAms share with ANE, the closer they are to Loschour vis-a-vis East Asians. Any alternative scenario would have to explain how this came about, if ANE root with ENA and NAms have no WHG.

On the other hand, its difficult to explain why so many rather basal pops can be modeled as Sardinian + Dai, but this in and of itself could be due to a variety of factors.

My own suspicion is that the tree model we have today is not detailed enough, and that 'Basal Eurasian' is a series of outgroups to crown Eurasian, some more divergent, some less, so it is paraphyletic. Or some other complex phenomenon.

This would help us explain the weird Stuttgart vs K14 figures as well, if K14 does in fact have only a little gene flow from the middle east.

Chad Rohlfsen said...

David,
I'm not sure if you saw it, but Felix said that it will take over a month to complete all of the Kostenki files.

Davidski said...

Well, the other option is to e-mail this dude and ask him for the Kostenki14 Bam or VCF files. These would only take a few hours to process.

ewillerslev [at] gmail.com

It's strange that they haven't uploaded the Bam and VCF at the CBS site yet, because they usually do. Maybe they will soon, or maybe they haven't published the link yet anywhere?

The Mal'ta and Anzick files are at these links. So there should be a similar Kostenki page as well.

http://www.cbs.dtu.dk/suppl/malta

http://www.cbs.dtu.dk/suppl/clovis

Chad Rohlfsen said...

I've emailed Eske and Martin. Hopefully, one of them can provide something.

Chad Rohlfsen said...

Perhaps, Kostenki's Basal is actually mostly of the UHG that is in the Middle East. He may only be in the single digits for actual Basal. It just comes back as NEOL, because that is where the great majority is found. Hence, his Basal and East African components. I believe that ANE k7 showed more WHG/UHG in North Africa, than was in modern Near Easterners.

Chad Rohlfsen said...

Looking back over Ust-Ishim, he is actually closer to Onge, Han, and Karitiana than he is to Malta and La Brana. Closer to Han than Karitiana. Maybe small amounts of Basal are present in both. Kostenki could have input into MA-1 and Native Americans. He is actually slightly closer to La Brana, than Malta. Just a hair though. Comparing the Onge to

Chad Rohlfsen said...

cont.. Comparing Onge, to any Western Hunter, it's not very close.

Chad Rohlfsen said...

http://ricco.popgen.dk/thorfinn/kos18octBlue.bam

Here you go!! Thorfinn said the ena will be updated in a few days.

Chad Rohlfsen said...

Per Thorfinn...

This bam contains the 7 best libraries. For the popgen analysis we removed 5bp from the ends of the reads.

Eduardo Pinto said...

Ust'-Ishim results

12.03% ANE
16.14% ASE
9.50% WHG-UHG
14.72% East_Eurasian
2.62% West_African
13.55% East_African
18.36% ENF
13.09% Oceanian


2.37% Amerindian
4.60% West_Asian
10.58% Australasian
3.12% Palaeo_African
8.14% Neo_African
3.10% Siberian
7.67% Southern
16.81% East_Asian
13.63% Atlantic_Baltic
29.98% South_Asian

Srkz said...

Ust-Ishim IBD (or IBS? Don't know how it is possible )) )
http://s017.radikal.ru/i438/1411/5a/a06eaaddfbd8.png

Bashkir 52,65 ---//Confidence: low
Kirgiz 52,25 ---//Confidence: very high
Buryat 51,89 ---//Confidence: high
Yakut 51,07 ---//Confidence: very high
Uygur 50,38 ---//Confidence: medium
Kazah 49,77 ---//Confidence: high
Uzbek 49,66 ---//Confidence: high
Altaian 49,44 ---//Confidence: high
Ket 49,12 ---//Confidence: very low
Selkup 48,43 ---//Confidence: high
Hakas 47,95 ---//Confidence: medium
Mari 47,58 ---//Confidence: high
Evenk 47,15 ---//Confidence: high
Han-North 46,88 ---//Confidence: medium
Dolgan 46,55 ---//Confidence: medium
Turkmen 45,61 ---//Confidence: high
Even 45,2 ---//Confidence: medium
Mongol 44,67 ---//Confidence: medium
Tuvinian 44,47 ---//Confidence: high
Mansi 43,97 ---//Confidence: medium
Saami 42,11 ---//Confidence: high
Moksha 41,14 ---//Confidence: very low
Tatar-Kazan 41,02 ---//Confidence: high
Tadjik 40,99 ---//Confidence: high
Udmurt 40,9 ---//Confidence: high
Chuvash 40,89 ---//Confidence: high
Nogay 40,14 ---//Confidence: high
Nganassan 39,89 ---//Confidence: medium
Erzya 39,83 ---//Confidence: medium
Finnish 39,75 ---//Confidence: very low
Estonian 39,58 ---//Confidence: high
Chechen 39,56 ---//Confidence: very high
Veps 39,03 ---//Confidence: medium
German-Austrian 38,72 ---//Confidence: very low
Russian-North 37,89 ---//Confidence: very high
Bulgarian 37,56 ---//Confidence: high
Belarusian 37,41 ---//Confidence: high
Komi 37,13 ---//Confidence: high
Ukrainian-East-and-Center 36,03 ---//Confidence: medium
Norwegian 35,63 ---//Confidence: high
Kumyk 35,48 ---//Confidence: high
Italian 35,46 ---//Confidence: very high
Ossetian 35,44 ---//Confidence: high
Karelian 35,35 ---//Confidence: high
Adygei 35,14 ---//Confidence: high
Balt 35,12 ---//Confidence: high
Abkhazian 34,39 ---//Confidence: very high
French 33,86 ---//Confidence: very high
Russian-South 33,78 ---//Confidence: very high
Lezgin 33,73 ---//Confidence: very high
Azerbaijani 33,73 ---//Confidence: high
Tatar_Lithuanian 33,4 ---//Confidence: very low
Russian-West 33,3 ---//Confidence: medium
Ashkenazi 33,27 ---//Confidence: high
Tatar-Crimean 33,14 ---//Confidence: low
Turkish 32,47 ---//Confidence: high
Shor 32,46 ---//Confidence: very low
Swedish 32,25 ---//Confidence: high
Hungarian 32,18 ---//Confidence: very high
Polish 32 ---//Confidence: high
Croatian 31,83 ---//Confidence: very high
Balkarian 31,72 ---//Confidence: very high
Iranian 31,6 ---//Confidence: very high
Greek 30,82 ---//Confidence: very high
Romanian 30,66 ---//Confidence: medium
Basque 30,48 ---//Confidence: very high
British 30,28 ---//Confidence: very high
Georgian 28,38 ---//Confidence: high
Armenian 28,36 ---//Confidence: high
Sephard 26,59 ---//Confidence: high
Sardinian 26,55 ---//Confidence: very high
Ukrainian-West-and-Center 26,08 ---//Confidence: medium
Greek_Azov 22,62 ---//Confidence: low

ryukendo kendow said...

Sikora has published a reply to Razib today.
http://www.unz.com/gnxp/the-k14-paper-an-author-speaks/

Davidski said...

Thanks for the bam link Chad. Here's the Eurogenes K15 for Ust-Ishim.

North_Sea 0.06
Atlantic 11.22
Baltic 0
Eastern_Euro 3.06
West_Med 4.82
West_Asian 0
East_Med 0
Red_Sea 3.36
South_Asian 30.75
Southeast_Asian 15.26
Siberian 2.01
Amerindian 2.19
Oceanian 10.97
Northeast_African 10.1
Sub-Saharan 6.22

Chad Rohlfsen said...

It's almost like he's basal to east Eurasian. Interesting....where does NO fall below him?

VOX said...

Hi David,

Is is possible to do some f3-statistics on Ust-Ishim and moderns. Perhaps it could give some insight into the whole Basal Eurasian thing.

Davidski said...

Yes, I just need to put it into my dataset. I'll do that later today.

If anyone has any well thought out ideas on the f3, f4 and D-stats to run using the high coverage genomes now available please list them here.

But it's better to use the higher quality genomes, and also maybe base the formulas on what we've seen already in the papers to date.

Chad Rohlfsen said...

I am wondering why WHG is more Onge like than ANE. That is strange.

I wonder if Ust-Ishim plus Kostenki equals WHG. Then, Kostenki plus some unknown Near Eastern UP equals UHG.

Maybe a Kostenki-Ust-Ishim-Loschbour/La Brana test would yield something.

Maybe, just for shits and giggles Kostenki-Onge-Loschbour/La Brana.

Chad Rohlfsen said...

I think that Sikora is thinking something like my previous post. Kostenki is possibly ancestral to something in BE. I think it is the UHG part.

Mbuti-Kostenk-Stuttgart

Mbuti-Loschbour-Stuttgart

Chad Rohlfsen said...

Excuse me, ancestral to something in EEF, not BE.

Krefter said...

"No, I don't know of any pre-Andronovo aDNA from Siberia apart from MA-1 and AG-2."

Ebizur, there's plenty.

http://www.ancestraljourneys.org/bibliography.shtml#Molodin2012

http://www.ancestraljourneys.org/mesolithicdna.shtml

Chad Rohlfsen said...

David,
What about Ust-Ishim-Kostenki-MA1?

Davidski said...

In what form though? You mean f3?

Chad Rohlfsen said...

Yes.
Then Ust-Ishim-Kostenki-Loschbour or La Brana.

Then,
Ust Ishim-Kostenki-Stuttgart on F3

for comparison something like..
Onge or Ho-Kostenki-Stuttgart

Something about the Onge, is looking quite Basal. But, an Eastern shift like we see with WHG, compared to ANE, on the Ust-Ishim paper.

I'm not sure if it will work, but for some reason ASI keeps popping up here. It makes me wonder if ANE has a lot of something Ust-Ishim or Onge like, in it. We need a UP South Asian! Big Time!



Davidski said...

By the way, this PCA might be useful in estimating ANE, WHG and EEF.

https://drive.google.com/file/d/0B9o3EYTdM8lQRy04NV9VcFZuNTg/view?usp=sharing

Chad Rohlfsen said...

Nice! Where should I imagine the exact location is? Left of the name, above, in the middle of the letters? Just curious. I'll see if I can get something for Bedouins and others with low ANE.

Davidski said...

Smack bang in the middle of each label.

Chad Rohlfsen said...

I guess that if it's to scale, then it looks as if Bedouins are closer to 60-65% Basal, and once we get above Armenians, or there about, we get even with Stuttgart levels again.

I wonder if a Mbuti, Kostenki, Bedouin f3 would be better than using Loschbour, La Brana, or MA-1.

Chad Rohlfsen said...

Like Matt, I am wondering if we have two Basals. One that is something like Ust-Ishim/Onge, and another that is typical in farmers, maybe more NE Africa, or Arabia. The way that Bedouins shift to the East, off of that Loschbour-Stuttgart line, is very strange. I noticed it in the last one too. It does it here, without South Asians. I wonder if that is a signal of something, or just issues with every PCA. You would think that Near Easterners would be more straight under Stuttgart, and shifting towards MA1. If Kostenki is very much like UHG, I wonder what kind of affinity it has with ASI folks. This is very interesting.

Chad Rohlfsen said...

David,
When you finish Kostenki, you should check it in treemix, for BE, and then if there is no BE in him, do a run with him admixing into Stuttgart. See if he is closer to the 56% than Loschbour. If I remember correctly the supplementary info had Loschbour fitting into Stuttgart at around 40-42%.

Chad Rohlfsen said...

Ust-Ishim
Harappaworld
Using 1 population approximation:
1 great-andamanese @ 25.363333
2 onge @ 29.846519
3 khasi @ 30.996717
4 bengali @ 32.152157
5 nepali @ 32.360126
6 nepalese-c @ 33.432529
7 up-muslim @ 33.926655
8 romanian-b @ 34.000465
9 bengali-brahmin @ 34.649441
10 bene-israel-jew @ 34.728195
11 singapore-indian-d @ 34.820019
12 brahmin-uttaranchal @ 35.098087
13 cochin-jew @ 35.497910
14 bihari-muslim @ 35.669674
15 pushtikar-brahmin @ 35.678307
16 sri-lankan @ 36.110191
17 gujarati-muslim @ 36.305901
18 nepalese-a @ 36.807880
19 kerala @ 37.236935
20 punjabi-jatt-muslim @ 37.401302

Using 2 populations approximation:
1 50% onge +50% puerto-rican @ 16.952904


Using 3 populations approximation:
1 50% onge +25% saharawi +25% tajik @ 11.136020

Dodecad v3
Using 1 population approximation:
1 Nepalese @ 17.769493
2 Sahariya @ 29.689220
3 Burusho @ 30.809431
4 Kharia @ 31.189213
5 Vaish @ 31.628696
6 Cochin_Jews @ 32.148209
7 Hazara @ 32.432648
8 Tharu @ 32.808144
9 Bnei_Menashe_Jews @ 33.106617
10 Kashmiri_Pandit @ 33.229652
11 Satnami @ 33.558006
12 Meghawal @ 33.836502
13 Srivastava @ 34.201458
14 Pakistani @ 34.656860
15 Sindhi @ 35.173508
16 Santhal @ 35.267445
17 Pathan @ 35.325813
18 AP_Brahmin @ 35.394745
19 TN_Brahmin @ 36.082317
20 Uygur @ 36.337429

Using 2 populations approximation:
1 50% Hazara +50% Sahariya @ 15.687673


Using 3 populations approximation:
1 50% Indian +25% Naxi +25% SANDAWE @ 9.918400


Using 4 populations approximation:
1 Morocco_S + Chenchu + Nysha + Vaish @ 8.426116
2 Japanese + Morocco_S + Chenchu + Vaish @ 8.479573
3 Tu + Morocco_S + Chenchu + Vaish @ 8.492227
4 Morocco_S + Aonaga + Chenchu + Vaish @ 8.510759
5 Morocco_S + Bhil + Nysha + Vaish @ 8.514538
6 Korean + Morocco_S + Chenchu + Vaish @ 8.542522
7 Morocco_S + Aonaga + Bhil + Vaish @ 8.571218
8 Morocco_S + Madiga + Nysha + Vaish @ 8.593592
9 Japanese + Morocco_S + Chenchu + Vaish @ 8.597424
10 Xibo + Morocco_S + Chenchu + Vaish @ 8.613555


MDLP k23b
1 Ayta_AE @ 24.783888
2 Nepalese @ 27.270012
3 Kensiu @ 29.925926
4 Tamil_Singapore @ 29.993927
5 Cochin_Jew @ 30.449663
6 Onge @ 31.218340
7 Pahari @ 31.865376
8 Mumbai_Jew @ 33.207047
9 Dhaka_mixed_popul @ 33.615238
10 Hindi @ 34.281342
11 Uygur-Han @ 34.523560
12 Jatt_Haryana @ 34.819286
13 Tiwari @ 35.455795
14 Pakistani_Pushtun @ 35.725113
15 Marathi @ 35.728867
16 Jatt_Muslim @ 35.853012
17 Mamanawa @ 36.317513
18 Vaish @ 36.851608
19 Brahmins_UP @ 36.884640
20 Spiti @ 37.032146

Using 2 populations approximation:
1 50% Onge +50% Puerto_Rican @ 13.927173


Using 3 populations approximation:
1 50% Ayta_AE +25% Hakkipikki +25% Puerto_Rican @ 9.896082


Eurogenes k15
Using 1 population approximation:
1 Afghan_Hazara @ 37.181583
2 Uygur @ 37.482956
3 Bangladeshi @ 37.949699
4 Uzbeki @ 38.291199
5 Burusho @ 38.814610
6 Afghan_Uzbeki @ 38.916122
7 Hazara @ 38.969475
8 Punjabi_Jat @ 39.612343
9 Brahmin_UP @ 39.939823
10 Afghan_Tadjik @ 40.071136
11 Tadjik @ 40.331684
12 Pathan @ 40.512333
13 Sindhi @ 41.588696
14 Kshatriya @ 42.665909
15 Afghan_Pashtun @ 42.912281
16 Afghan_Turkmen @ 43.073124
17 Gujarati @ 43.435024
18 Austroasiatic_Ho @ 43.635574
19 Turkmen @ 44.208851
20 MA-1 @ 44.226265

Using 2 populations approximation:
1 50% Austroasiatic_Ho +50% Mozabite_Berber @ 18.816782


Using 3 populations approximation:
1 50% Austroasiatic_Ho +25% French_Basque +25% Maasai @ 12.379299


Using 4 populations approximation:
1 Austroasiatic_Ho + Austroasiatic_Ho + French_Basque + Maasai @ 12.379299
2 Austroasiatic_Ho + Austroasiatic_Ho + French_Basque + Sandawe @ 12.699069
3 Austroasiatic_Ho + Austroasiatic_Ho + Maasai + Southwest_French @ 12.856832
4 Austroasiatic_Ho + Austroasiatic_Ho + Maasai + Spanish_Aragon @ 12.875328
5 Austroasiatic_Ho + Austroasiatic_Ho + Maasai + Spanish_Castilla_La_Mancha @ 13.053628

Oddly, he seems to have affinity to South and East Asians, with a push away from anything with ANE, on more than on population.

Chad Rohlfsen said...

correction.. 'one' population

ryukendo kendow said...

@ Chad
Those are wonderful results! I think it supports somewhat the position of U-I as one of the first few people on the ENA half of Crown Eurasian, whose variation is best preserved in India and SEA negritos today.

@ Davidski
I have some suggestions:
1) I think THREEPOP stats for Ust-Ishim and K14 would be very interesting.

This should cover most bases using f-stats once through.

2) D-stats might help us to place Ust-Ishim on the ENA tree, and clarify if he left any descendants:
i. comparing how close Usty are to ENA populations vs Loschour.
ii comparing how close ENA are to Usty vs Loschour.
iii. Comparing how close East Asians are to U-I vs. Onge.
iv. Comparing how close East Asians are to U-I vs Papuan.
v. Comparing how close Onge are to U-I vs Papuan.

These above can be investigated using f-stats too.

3) I think D-stats comparing K14 with Loschour and Mal'ta would be good as well.

Also, if K14 did introduce UHG into MidEasterns, then it might be possible to model West Asian pops as Bedouin + K14 in f3, with admixture increasing to the north.

To see if it really is the same Basal as Laz or something else, we can try fitting K14 as Loschour + Test in f3.

Balaji raised the series of (Middle Eastern; Sardinian, Dai) figures. I think a test fitting a series of West Asian pops as Sardinian + Test might help us clarify what it is we're seeing.

Lastly, we can attempt a correlation like the authors of this paper did: first, have D-stats to see if West Asian populations are closer to Onge or Ajvide. Then attempt to correlate the scores of West Asian pops with the 'Papuan' component ADMIXTURE produces at low K, typically at K=5. If the correlation is high, then the ASI in Middle East might receive some circumstantial support. Once this is done we can then look as K14's basal with a clearer idea.

ryukendo kendow said...

@ Davidski
Sorry, I remembered you don't have Onge in your dataset.

For 2), we could try replacing them with a south Indian Tribal, while for the last experiment in 3), we could replace the references with Karitiana and Papuan instead.

Krefter said...

I put Table S7 from Seguin-Orlando et al. 2014's Supplementary info in a new format, so that it can be more easily read. I'm going to do the same to other tables. It's important information but annoying to have to find a link to the paper and take info out of hard to read formats.

https://docs.google.com/document/d/1PfparM8qpJJ5b4Gq6UWJbRP7cBtjqX7i4Odt1Rej9Hs/edit?usp=sharing

By region: Europe, middle east, central Asia.

https://docs.google.com/spreadsheets/d/1sGychnMdEMg9UvW5oPTYtWqi7ZOG7p_ZU1uzzXoCm4g/edit?usp=sharing

Seinundzeit said...

That's very interesting, so David was on to something when he speculated that his K7 "ASE" component represented something "basal" (and why it behaved very differently in comparison to the Reich et al. "ASI" construct, which is supposed to be very specific to South Asia. By contrast, the K7 "ASE" component is found almost everywhere in Eurasia). In the paper, it seems the closest living population to Ust-Ishim are the Onge (but not by much, a minor difference compared to other ENA populations).

ryukendo kendow said...

@ Kruefter
Thanks! Makes life so much easier.

@ Davidski
Actually, after some thinking, the last test in the series I proposed is uninformative.

If we're trying to see if there is ENA influence from an ASI branch in the middle east, assuming that the ASI influence is occurring after the ASI-Dai split, we can attempt D stats for European and Middle Eastern populations between Dai and Onge. Since we don't have Onge we can try Papuan, who are 50% Onge-like and 50% 'other', by Reich's model.

European pops will be equidistant between the two, because Basal, WHG and ANE all split off before ENA split from ASI/Papuan. Or, if there is something weird going on with papuans as I suspect there is, Europeans will be closer to Dai. The informative comparison occurs between Middle Eastern Populations against European ones. If ME pops are closer to Papuan in the papuan-dai comparison than Europeans are, we might be seeing something to vindicate that the widespread 'Papuan-like' component at low K is real.

If the 'Eastern influence' is some kind of basal ENA that split off before the Dai-Onge split, or even another outgroup to (ENA-WHG-ANE) not the same as Stuttgart's Basal, this test might still be informative, but only if we assume that this influence is stronger in papuans than in Dai.

Thanks if you could try this. What are your thoughts?

Also David, I understand there are risks, but I think we're going to need the Onge genome to go in your dataset for more resolution in our tests pretty soon once more results from Central Asia/Siberia emerge, which Sikora hinted at.

Davidski said...

Isn't Ust'-Ishim the perfect Onge? It doesn't have any Denisovan or Basal, and its Neanderthal is lower than among East Asians, so it's the ideal Eurasian control. Or am I wrong?

By the way, keep in mind that BedouinB have a lot of Sub-Saharan admix, maybe as much as 8%. So I don't know how useful they are as references in formal stats.

But I think that TreeMix will very easily show us how Kostenki14 and Ust'-Ishim compare in terms of Basal Eurasian.

ryukendo kendow said...

@ Davidski
Agree that he is the 'perfect' Crown Eurasian for any outgroup detection. I think we need more resolution within the ENA clade though.

We can use Ust-Ishim too, but we have no idea what he will stand in for. If Middle Easterners are closer to Ust-Ishim in a Ust-Ishim-Dai comparison than Europeans are, it isn't clear what that means.

I'm trying to figure out if there is some ENA contribution into Middle Easterners that distinguish them from Europeans, if your ASI/ASE theory is correct. To do this we need to freeze ENA's pulling effect on Europeans due to them having more Crown Eurasian; so both references have to be ENA, with one with putative contribution to MEs but not Euros and another having no contribution to either MEs or Euros.

If MEs are indeed closer to U-I in a U-I/Dai comparison than Europeans are, this might be a big deal, but only if we know the position of U-I in the ENA tree, and for that we need Onge.

Also, I suspect that a large number of old Eurasian aDNA in Crown Eurasian is going to score nonspecifically in Indian/SEAsian/Oceanian components in ADMIXTURE and calculators based upon it, producing the approximations we see above, and Treemix is just gonna shift such genomes around randomly, like it did for Mal'ta, due to deep branching. So we have to have formal ways of segregating influences in India.

How about Yemenite Jews?

Balaji said...

Davidski and Ryukendo,

The famous TV astrophysicist Neil deGrasse Tyson infamously said regarding charges that he had fabricated quotes by President George W. Bush, “The absence of evidence is not the same as evidence of absence”.

http://freethoughtblogs.com/dispatches/2014/10/01/how-not-to-respond-to-criticism-or-why-accuracy-matters/

That certainly applies to statistical tests. Some tests may not be powerful enough to detect effects that we are looking for. Perhaps that is why the D statistics that you calculated, did not show that ANE and ENA formed a clade to the exclusion of WHG.

Consider the following f3 statistics.

Maasai;Dai,Mbuti_.Pygmy -0.00534596 0.000253622 -21.0784

The z value of 21 indicates it is highly significant The Maasai have some Middle Eastern ancestry and Middle Easterners and Dai are part of one clade – that of all non-Africans. There was only one OOA event that gave rise to all non-Africans.

Turkish;Dai,Sardinian -0.00317536 0.000163154 -19.4623

Turks have some East Asian ancestry and therefore this statistic is highly negative.

Gujarati2;Dai,Georgian -0.00245376 0.000182314 -13.4589

Here the Dai are a representative of the (ASI,ENA) clade.

Spanish;Dai,French_Basque -0.000975007 0.000124464 -7.83365

In this case, we have two genetically and geographically closely related populations, They have the same EEF, WHG and ANE components with some differences in the proportions of the various components, The Dai here can only be playing the role of a representative of the (ANE,ENA) clade.

That ANE and ENA form a clade to the exclusion of WHG does not mean that ANE is closer to ENA than it is to WHG. It only means that ANE is closer to ENA than WHG is to ENA. A look at a PCA will make this clear. Middle Easterners and Europeans with varying amounts of AME, WHG and ANE are all bunched together as against East Asians on the other side.

Chad Rohlfsen said...

I've asked Reich for any bam files on Andaman/Onge, from his 2009 study. We need to see if they or Ust-Ishim, are closer to no preference for East or West Eurasians.

Davidski said...

They're available, but only on request after signing a waiver, and I don't want to do that.

Ponto said...

Look Balaji, what you quoted some dickhead supposedly saying might make sense to you, and him but it ain't a scientific statement only sophistry. No one can disprove God or Gods exist or Aliens regularly visit Earth for their holidays.

Stick to scientific statements not sophisticated bullshit.

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