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Tuesday, May 3, 2016

For a typical West Eurasian PCA, the Epipaleolithic is the final frontier


My dataset now includes the samples from Qiaomei Fu et al. 2016. They're freely available at the Reich lab website here.

Below is a Principal Component Analysis (PCA) featuring 10 of the freshly sequenced genomes from the paper classified as Epigravettian, Epipaleolithic and Mesolithic, as well as the Siberian (late?) Upper Paleolithic forager Afontova Gora 3.

I did try to include all of the new genomes from the paper on the plot, but most were getting results that didn't make any sense. They were simply too old and too far removed in terms of genetic structure from present-day West Eurasians.

But that's OK. I can analyze them with formal statistics, and promise to do so vigorously in the coming weeks.

By the way, Villabruna is the ~14,000 year old genome from Italy belonging to Y-chromosome haplogroup R1b. Gioiello, you still breathing?

See also...

Ice Age Europeans in a global PCA

79 comments:

Karl_K said...

Looks good. Villabruna almost looks like a typical WHG to me.

Davidski said...

In the paper they basically renamed the WHG cluster as Villabruna. I guess it was the earliest sample of this type.

Karl_K said...

For clarity's sake, it's a good thing that the R1b WHGs didn't expand so much with the WHG autosome.

Otherwise people might get confused and think that this means the R1b found in Europe today is from this WHG population. Am I right?

Nirjhar007 said...

Dave,

Do you know of any upcoming aDNA say...within 6 weeks or so?.

Davidski said...

Not really, but the SMBE 2016 abstracts will be out in a couple of weeks, and they should be pretty good this year.

Nirjhar007 said...

Uh aDNA from which sites you are expecting? there will be EE?.

Gioiello said...

Davidski, I avoided writing in these two days, I have written for pretty ten years. The most ferocious things I wrote on my FB account, so from there no one may ban me.
And I haven't all your knowledge about autosome etc. I used only the monophiletic Y and mt in my analyses. I wrote only a few words to one of the few friends I have on these blogs, banned pretty as much as me:
"Dartraighe, but don't do like Jews, who, when they find their Italian origin, call it "Mediterranean Islands" (see the shit that is DNA.land).
It happened the other way around: are the Northern countries that were peopled from the Italian Refugium:
"EPIGRAVETTIAN The late glacial industries of Italy from 20,000-8000 bp, which evolved into the Mesolithic. It is divided into early (20,000-16,000 bp), evolved (16,000-14,000 bp), and final (14,000-8,000 bp) phases. Epigravettian was followed by the Sauveterrian and Castelnovian in the 7th millennium BC. Epigravettian cultures developed contemporaneously in various parts of Europe, notably the Creswellian in Britain".
Certainly Villabruna has nothing to do with Eastern Europe and less with Middle East. My victory is complete. All my enemies defeated, and you have always been one of the few friends".

Nirjhar007 said...

Can you give your FB link please?:).

Olympus Mons said...

Davidski. Cant seem to find Satsurblia. is it in there?

AWood said...

@Karl_K

There was a rebound of WHG after the collapse of LBK, just look at a Bell Beaker genomes. I don't see any reason why R1b was anything other than part of the WHG-EHG continuum. I was expecting an eastern origin of R1b, but maybe it was always in Europe, that is, west of the Urals.

Olympus Mons said...

If Bell Beaker genomes are still a valid marker for current R1b expantion in Europe, yeah, look at Bell beaker genomes for germany and what is that sub saharan part in them?

Olympus Mons said...

@AWood

When you say eastern, where do you mean?

I had it as given that everybody expect it to be either middle Volga or Dnieper basin...

ghostnorris said...

David, are you planning to run a global PCA with the new samples? It'd be interesting to see where the pre-Villabruna samples plot (since they make no sense on a West Eurasia-only run).

Gioiello said...

@ Nirjhar007

"Can you give your FB link please?"

If you are on Facebook and ask for my friendship, you may read and write on my page...but we write frequently also in Italian. Anyway this is what I wrote as to you:
"Other persons who wrote these posts on “Eurogenes blog” are unknown from me, but I would thank here Nirjhar007/parasar, an Indian who exchanged some letters with me on Anthrogenica and elsewhere, even though I said always to him that Indian Indo-European R1a weren't born in India, as you believed and hoped, but came from the Russian plain",
because I quoted what you wrote here: "Capra,
Yes I am happy for him. He had professional knowledge and passion also. Now He seems to be proven right. Who knows perhaps 20000 yo old samples from Italy will also show R1b?"
and your request could get a positive answer, as, if the Davidski's analysis is right, it seems that the R1b1/PF6401+/PF6412+/P297- of Villabruna is in Italy from many thousands of years.

Ariele Iacopo Maggi said...

Even if this paper opened the possibility that the italian refugium is the one that had the biggest impact in europe after the LGM (Villabruna...), and it's possible that the italian peninsula had some r1b in the same time period (even if it was less then 5%) these facts do not imply (at all) that most of the modern "western" R1b is from that period and that population. Maybe after the LGM some r1b males wandered from northern Italy to Ukraine and had a strong r1b founder effect when they mixed with a pre-EHG population that was rich in ANE. This possible sequence of events does not contradict (at all) the fact that most of the r1b in western Europe (and Italy) is from a bronze age invasion from the russian steppe (a theory that is basically already confirmed).

Davidski said...

I'll try a global plot tomorrow.

Gioiello said...

@ Maggi

I have no problem in accepting what you say, but I opposed firstly to all who said that R1b came from Middle East and all came from Middle East, the famous Ex oriente lux, and I said that there were migrations from and to and not only from East to West. At the same time I opposed to all those who said till yesterday that we wouldn't ever have found R1b in Western Europe before the invasion of the kurgans, and often I said that there were migrations from and to also from West to East etc. Anyway, in saying that R1a abd R1b derived from WHG I was right it seems.
Anyway mine is a theory, and I often hinted in the past to Higgs and his theory of the boson. The problem for my opponents, and the skeptics as you too, is that they found R1b exactly where I said that it should have been searched. Of course this is only the beginning. I am waiting that all my other hypotheses are checked, and in my hypotheses R-L51 should come out from Tuscany and not from Eastern Europe...

Arch Hades said...

AfontovaGora3 looks quite ANE like, "Villabruna" on the other hand IS WHG.

But I'm curious where the "individuals between ~37,000 and ~14,000 years ago descended from a single founder population which forms part of the ancestry of present-day Europeans" plot. If it makes no sense on a West Eurasian PCA then can we still tell which modern Europeans have the most ancestry from them? Or can we possibly model WHG as a mixture of them and something else? Is WHG completely new to the region, or was it just a mix of those 37,000 YO Europeans with a new southern strain? That's my bet.

George Okromchedlishvili said...

@Arch Hades:

If you look at tree modelling they arrive at WHG being a mix of predominantly new invading population and older survivors related to Goyet and Iberian refugium.
This would explain why ENFs can be modeled as WHG plus something else as they have absorbed WHG-related West Asian group on their way across Middle East to Europe

Matt said...

Re Italian refugium, It seems tough to me to explain the Villabruna cluster as just from the Italian refugium rather than elsewhere further east, because you would then need

a) to explain why Villabruna differs from the earlier "Vestonice" Gravettian already previously established in Italy, without migration

b) explain why the Villabruna cluster has increased relatedness to the Near East and East Asian populations

I don't think you can explain these without it ultimately having a different origin, probably South East (Ukraine seems less likely because of climate). Possibly there was population structure in Italy and the Villabruna types were there all along, and then expanded elsewhere (including the Near East, via Anatolia), but it does not seem that likely.

@ Arch Hades

" If it makes no sense on a West Eurasian PCA then can we still tell which modern Europeans have the most ancestry from them?"

I expect when we see the formal stats, it'll probably be Northeast Europeans and Basques again. But the difference will probably be very shallow.

E.g. based on the fraction of GoyetQ116-1 "Aurignacian" ancestry in the El Miron, Loschbour and La Brana apparently look about 25% El Miron "Magdalenian" cluster (while some of the Villabruna / WHG cluster have none). Then probably only 10-25% of modern European ancestry is WHG / Villabruna, varying from lowest in Southern Europe to highest in North East, so that's like a variation from at most 2.5% "Magdalenian" to 6.25% "Magdalenian" (and probably less). So I would not expect that to lead to very big differences in affinity to them. Might be enough to inherit some unusual novel mutation that occurred in these populations, but not like a big affinity.

For the Vestonice "Gravettian" cluster it's even worse, since they don't seem to contribute to Villabruna or even El Miron at all.

If the patterns are different in modern Europeans (perhaps due to different amounts of El Miron cluster in different WHG), then that will be a turnup for the books.

Krefter said...

"For a typical West Eurasian PCA, the Epipaleolithic is the final frontier"

Great Title choice. By the Epipaleolithic or Holecene or post-Ice the genetic diversity is what we have today just at differnt proportions. Our pre-Ice age people, except MA1, are mostly dead relatives.

Karl_K said...

@Krefter

"Our pre-Ice age people, except MA1, are mostly dead relatives."

Is MA1 still alive? Very interesting.

Chad Rohlfsen said...

These are migrants. Plain and simple. They weren't hiding in Western Europe. Everyone in western, southern, and Central Europe was roughly the same. This is a rather uniform group across Iberia to Germany and Hungary. Western HGs like La Brana and Loschnour have more UP ancestry, consistent with these people coming from E SE.

Ariele Iacopo Maggi said...

Ukraine seems to me a rather odd place to be the origin of western HG (Villabruna), Villabruna could be the south-eastern strain of the first sapiens that came in europe, they remained hidden for 20k and then pop out after the LGM passing from the balkans or Italy, or maybe they came from the east, maybe anatolia, the levant or north africa, I don't see Ukraine as a possibility (cold ass climate in the LGM period, low pop) but you never know.

Matt said...

We could say the likes of the Gravettian "Vestonice" cluster are dead relatives, because we have later populations who don't model as descended from them, and who are better contributors to modern people. And to a lesser extent (just about less than 100%) the Magdalenian "El Miron" group.

But I think we can say the same thing about the Malta-Buret culture that MA1 came from. Just as in Europe, in Siberia we have AfontovaGora3 who does not seem descended from Malta1's people (looks like a sister lineage?), and who is a better contributor to modern people (at least EHG and Native Americans). As more samples accumulate from ancient Siberia, and we understand the structure there in the same way as this paper has made the European structure apparent, this should become more obvious. So MA-1 we can also classify as from a relative lineage that died out.

Alberto said...

In Europe everyone was a migrant at some point, and everyone came from the east. But that "Red Lady of El Mirón", 18,700 BC, is already some 50% La Braña, and unlike the other Magdalenians who were mtDna U8a, she is U5b like the other WHGs. So that's a terminus ante quem, not for Europe, but for Iberia, at the west end of Europe, for the arrival of WHGs.

Satsurblia, 13,300 BP, in the Caucasus, already had Basal Eurasian admixture. So one could assume that Basal Eurasian was in the Near East during the LGM (not surely, but quite possibly).

This could mean that WHGs entered Europe before the LGM if they came from/through the Near East, and up to during the LGM if they came from Eastern Europe/West Siberia.

D(Mbuti, MA1; Villabruna, Vestonice16) Z=0.7
D(Mbuti, MA1; Villabruna, GoyetQ116-1) Z=0.3
D(Mbuti, MA1: Villabruna, ElMiron) Z=-0.4

There doesn't seem to be any special relationship between MA1 and WHG (so the close to 40% non-ANE in MA1 -estimated from Karelia_HG being some 60% WHG-like and 40% ANE- is some generic/unknown West Eurasian).

Looks more like WHG came from/through the Near East, but before the Near East got Basal Eurasian admixture, which means probably before the LGM.

Ariele Iacopo Maggi said...

"Looks more like WHG came from/through the Near East, but before the Near East got Basal Eurasian admixture, which means probably before the LGM."

I'm worried that the first ancient dna from the very ancient near east is going to disprove that. The middle east is a open region, Europe had barriers, seas and mountains. (CHG and anatolian farmers had basal already around 10000BCE) And I don't see where basal eurasian could have remain hidden in the middle east for 40.000 years without encountering the speculated populations. And if the modern near east is 20/40% whg that alone could explain the affinity with Villabruna that they discovered in this paper. I think it's a case of Occam's razor. Where was basal eurasian for 40.000 years? And why had such a big impact only much later? It's easier to think that it always been in the near east, and Villabruna is only the sister clade of the pre-whg europenas and they lived in south-eastern europe or in the italian refugium (maybe some islands).

Ryan said...

What branch of R1b is Villabruna from?

Davidski said...

I got rid of one of the samples from the plot. It didn't have enough markers for a reliable result.

I'm working on the global PCA now.

Rob said...

@ Ariele & Alberto

I think (put simplistically) that the "proto-WHG" people who contributed the 60% (whatever the exact figure is) mixed with Magdalenians from the Franco-Cantabrian refuge to 'create' WHG of the Late Glacial & Mesolithic. I agree with your hunches, and that of Chad, that they came from southeastern Europe, hence they're closer apparent affinities with NE. But of course, wholly lacking BE - which we know was present in the south Caucasus / E Anatolian foragers, and must have also been present in the incipient Natufians, means that they were in Europe (or at least in SEE) since before the LGM.

Alberto, if you suggest that a BE -type population expanded into formerly WHG like Near Eastern groups, where did they come from ? I don't recall reading about a population turnover in the N.E. during the LGM (although I haven't read extensively on that matter/ region).

About Malta-1. I recall having some extensive debates with the odd contributor who had convinced themselves that MA-1 represented some kind of continuity in Siberia. it is even more obvious now that it doesn't, and Afantova-Gora represents a new population moving into south Siberia. I'd bet AF-G will be put aside still once we get a better proxy for the groups which admixed into the WHGs of eastern Europe (quite probably also in the Late Glacial / early Mesolithic period (14-8 kya)

Davidski said...

Yeah, that's why Afontova Gora 3 was put in the Malta cluster, because obviously it represents a new population in Siberia that migrated there during the peak of the Ice Age. Haha.

Rob said...

Yes, the same population cluster, but this doesn't imply population continuity in the specific region around Mal'ta, as the fine-scale analysis with haploid lineages clearly suggests some break.

And the Peak of the LGM was 22-19 kya. AF-G dates to 17 kya, so after the LGM.

So it seems that Mal'ta was just an early northern Siberian offshoot which became extinct with the onset of LGM, and replaced by very similar groups, from perhaps not so far away.

Tobus said...

The SLC pigmentation genes don't show any surprises, although most of the samples lack coverage. Those with coverage are:

SLC24A5 SLC45A2
Bichon GG CC
Kotias AA CC
Satsurblia AA CC
Motala12 AA --
Villabruna GG CC
Vestonice16 -- CC
Kostenki14 GG --
Muierii2 -- CC
Vestonice13 -- CC
Ostuni1 GG --
ElMiron GG CC
AfontovaGora3 -- CC
Ranchot88 GG CC
GoyetQ116-1 -- CC
Malta1 GG --
Hungarian.KO1 GG CC
LaBrana1 GG CC
Oase1 -- CC
Karelia AA GG
Loschbour GG CC
UstIshim GG CC
Stuttgart AA CC

Nirjhar007 said...

Gioiello,

I am not Parasar :) , I know him but not him . I thank you for your words. Yes, I will look forward in reading your FB posts . I at the moment don't suggest an Indian origin of R1a and also surely don't suggest, that R1a-Z93 came in the Subcontinent from some hypothetical steppe migration, which fail to provide any reliable evidence.

Thankfully several aDNA sampling and testings are happening as we speak. I am sure something of epic proportion is in the making.

Regards

Gioiello said...

@ Iacopo Ariele Maggi
“I'm worried that the first ancient dna from the very ancient near east is going to disprove that. The middle east is a open region, Europe had barriers, seas and mountains. (CHG and anatolian farmers had basal already around 10000BCE) And I don't see where basal eurasian could have remain hidden in the middle east for 40.000 years without encountering the speculated populations. And if the modern near east is 20/40% whg that alone could explain the affinity with Villabruna that they discovered in this paper. I think it's a case of Occam's razor. Where was basal eurasian for 40.000 years? And why had such a big impact only much later? It's easier to think that it always been in the near east, and Villabruna is only the sister clade of the pre-whg europenas and they lived in south-eastern europe or in the italian refugium (maybe some islands)”.

Please tell everyone that. even though we live at a few kms, we don't know each other. Anyway I thank you for your contribute.

@ Nirjhar007
I apolgize in identifying you with Parasar, but, if I hadn't said that, I wouldn't have know that it isn't true and I would have thought to you as Parasar. He was one of the few to remain opened to my theories on Anthrogenica, for that I thought you were the same.

Krefter said...

@Everyone,

Here are some more important details I've learned reading the paper.

>Czech/Austria/South Italy/Romania(30k) are closer to each other than with anyother ancient Europeans. They don't have a particularly close relationship with WHG, but it's slightly closer than their relationship with Upper Palaeilthic Europeans.

>Beligium(35-30K) and WHG has a close relationship with Spain/Germany(19k-15k). Spain/Germany(19k-15k) are very close to each other and might decend from the same population.

>13-10k France/Germany are WHG. It looks like a rapid replacement by WHGs.

>Because of all the new Paleo Western European genomes, we know that EHG didn't just have genric West Euroepan ancestry, but from a specific branch(WHG). This is key. As much as ANE has been associated with WHG it's actually very differnt, because they had been separated for maybe 40,000 years. So, EHG was in a very real sense a hypird of North Asian and European population.

Krefter said...

Two more things.

I think La Brana-1 might have African ancestry. This is because every Eurasian is more distant from him than other WHGs. Has anyone tested this hypothesis? What we would need to do is do a very thorough test on all Africans. If he does have African ancestry, we should expect there to be a modern African population that shares decent from the same African population.

The 30k Romanian who has affinity to 30k Central Europe/Italy had mtDNA U6. So, we're seeing mtDNA U5, U2, U8, and U6 in the same Upper Paleo European population. U6's old history in North Africa evident in modern mtDNA structure, points towards populations related to Paleo Europeans living deep in Asia and maybe Africa 30,000 years ago. We already know their distant relatives(ANE) were living at the Eastern edge of Asia, so it isn't unbelievable that they were living in the Middle East and Africa.

Karl_K said...

@Krefter

"I think La Brana-1 might have African ancestry. This is because every Eurasian is more distant from him than other WHGs"

But there is no reason to believe that it is African ancestry. It could be any unsampled non-WHG ancestry.

But more to your point, I totally agree that pre-Neolithic North African genomes would be very interesting. It looks like there were early back migrations, so the turnover could be as complex as in Europe.

ryukendo kendow said...
This comment has been removed by the author.
FrankN said...

I have summed up the study's findings concerning "WHG ~ Near Eastern", "population replacement" etc. in the previous thread. They don't find anything of this, just signs of admixture: NE (North African?) during the UP, "East Asian" during the Mesolithic.

@Matt: "Vestonice" didn't die out, at least not completely. They (anachronistically) model it as 25% Vilabruna, indicating strong Proto-WHG contribution, and the fact that Proto-WHG was already present in CE 30 kya (c.f. Fig. S6.6).

Uniparental markers help for a better understanding. Except for the Vilabruna R1b, CT (xIJK) in Vestonice 13, and C1a2 in La Brana and Pavlov (CZ,30 kya), all European yDNA is I or upstream. I has been around since at least 32 ky (Cioclovina 1, RO), and most of the downstream differentiation (I1; I2a1/a2 etc.) is essentially restricted to Europe. Obviously, CT/C1a2 was crowded out by I during the UP, but that was an inner-European (proto-WHG) shift, no external turnover. The I2a1 substructure, with I2a1a peaking on Sardinia, and I2a1b in the Western Balkans, suggests an I2(a1) refugium in/around Italy, and I becomes frequent north of the Alps during the Epipaleolithic (HohleFels, Burkhardshöhle, Bichon). Looks like I was more successful, a/o because of geographic centrality, in post-glacial recolonisation than C1a2, which may have found its main LGM refuge in Iberia.

On mtDNA see, in addition to Alberto and Krefter the extensive discussion here: /eurogenes.blogspot.de/2016/02/ancient-european-mito-genomes-suggest.html

The main issue here is U5 vs. U8(a/c). Both hgs have been found in Vestonice, and are as such "Basal European", "proto-WHG" or however one wants to call it. No apparent sign of intrusion, rather "out of Europe" expansion (U5b* in Siwa Berbers, U5b1b in Fulbe and Yakuts, U8b in Jordan etc.).

U8(a) still dominates the Magdalenian until ~ 14,5 kya (Burkhardshöhle, 50 SE Stuttgart), but is replaced by U5a/b in Mesolithic SC Europe, incl. Falkenstein, 15km W of Burkhardshöhle. So at least in SW Germany there is a break on the mtDNA side, which seems to drive the El Miron - Vilabruna distinction.
The break coincides with the cooling of the Older and Younger Dryas (13.5-11.7 kya), which has resulted in a temporal hiatus/ cultural break elsewhere, e.g. Hamburgian vs. Ahrensburgian. The most parsimonous explanation, as for yDNA, is U5 being more successful in re-colonising Europe after the Younger Dryas than U8.
For mtDNA, it is more difficult to identify LGM/Dryas refugia. U8 was present in pre-LGM Italy (Paglicci 133), U5b in Late Glacial Iberia (El Miron) and with La Brana (U5b2c), but also in Italy (Paglicci 71, U5b2b, 18.6 kya). OTOH, U8a is today peaking in Basques, European U5b1(e) with Hungarians, Czechs and Slovaks [c.f. Loschbaur U5b1a], U5b2a with Czechs, Slovaks and Poles. Obviously, a quite complex history of (female) migrations, which requires further aDNA to be fully understood.
Nevertheless, we have a Late Glacial sequence of U5b2b finds from/near the Italian Adriatic coast (Paglicci 71, Vilabruna), setting forth pre-Younger Dryas into the French Jura (Rochedane), and finding Younger Dryas refugium in the Provence (Iboussieres) that supports a narrative of strong Late/Post Glacial expansion out of the Adriatic refugium (N. Italy & W. Balkans), possibly also Transdanubia [Vilabruna is located on a major Adriatic-Transdanubian connection along the Piave and Drava rivers].

Gioiello said...

@ FrankN

Great (whoever you are).

Alberto said...

@Ariele, Rob

Yes, the fact that we have WHGs in Europe and that Near Easterners were a 50%50 mix of WHG/UHG and Basal Eurasian is still quite a problem to explain.

Either there was a big move from WHGs to the Near East around the LGM, or there was a big move from Basal Eurasians to the Near East around that time too (from where??). Both scenarios are difficult to justify archaeologically. So I guess only ancient DNA from the Near East will solve that question.

The clues I'm trying to follow here (still very preliminary), are:

- We have some 20 samples from Europe from between 40,000-26,000 BP, and none of them is a WHG.

- The next sample we have is from 18,700 BP, ElMiron, and this one is a mix of the later Magdalenians and WHGs (those Magdalenians themselves could have been in Europe since at least 35,000 BP, since GoyetQ116-1 from that time seems to be half "Magdalenian".

- Then we have from 15,500-14,600 BP 6 Magdalenian samples, who seem to be an extinct type.

- After 14,000 BP all are WHG.

So it looks like WHG entered Europe sometime after 25,000 BP, and had reached Iberia at least by 18,700 BP. They were not specifically related to the "western" part of MA1, but they are specifically related to the "northern" part of Near Easterners. So the scenario I'm suggesting is that WHG entered Europe from the Near East just before the LGM and expanded through the south of Europe (which if they came from the Near East makes sense). They survived in Southern Europe during/after the LGM and later expanded to the rest of Europe and in the end were the only survivors.

Meantime, in the Near East, a Basal Eurasian population appeared (from deep into the Arabian Peninsula?) and mixed with the WHGs there around the LGM.

Honestly, not a great narrative, but with the data available I don't see a better way to explain how the WHGs appeared in Europe around 24-22K BP, but likely not coming from the Eurasian steppe/forest, and why ancient Near Easterners have 50% WHG ancestry (plus another 50% Basal Eurasian).

ryukendo kendow said...
This comment has been removed by the author.
Rob said...

In light of a few comments, what are peoples thoughts about

* the position of the Motala's, and how it fits now into the EHG - WHG continuum

* Could la-Brana's position be explained by higher retained El Miron input (not surprising given it's Iberian location, and C1 lineage)


@ FrankN

". The I2a1 substructure, with I2a1a peaking on Sardinia, and I2a1b in the Western Balkans, suggests an I2(a1) refugium in/around Italy, and I becomes frequent north of the Alps during the Epipaleolithic (HohleFels, Burkhardshöhle, Bichon). "

I don't think this is quite that simple. To be sure, I2 haplogroups swayed around significantly after the Mesolithic so we would be falling into a trap by looking at modern lineages and thinking it mirrors events 10000 years ago. And your position seems a little Italocentric, and have not considered the possible inputs from outer refugia ;)

ryukendo kendow said...

Hmm Alberto, actually your scenario would work. I went to check and Satsurblia (13.5KYA) is not as old as I remembered. So Razib's idea of 'Middle Eastern Villabruna' is still in play.

Just to add another parameter, there is little evidence of a cline of Neanderthal ancestry associated with differing levels of Basal or Crown Eurasian, so Basal Eurasian would have to be placed firmly in Eurasia; where it was specifically is of course a mystery as of now.

ryukendo kendow said...
This comment has been removed by the author.
Grey said...

A weird thing i noticed ages ago that seemed too far fetched at the time (as no R1b had been found in the west)(and still does seem a bit far-fetched but the Italian R1b find makes it slightly less so) is

if you look at R1b distribution

https://upload.wikimedia.org/wikipedia/commons/f/f2/R1b-DNA-Distribution.jpg

it looks like it expanded from the west from an epicenter in the sea south of Ireland and west of Brittany - which obviously makes no sense.

However the odd thing is if you look at a map of Doggerland

http://cdn.zmescience.com/wp-content/uploads/2015/01/31836.jpg

that epicenter in the middle of the sea is pretty much exactly on the SW Doggerland coast between those two rivers.

The thing about that position is, was the Gulf Stream a thing at that time? i.e. might the climate along that stretch of Doggerland coast have been relatively mild?

Then after the sea started encroaching an escape into the Franco-Cantabrian refuge for the Iberia connection?

Alberto said...

@Rob

Maybe La-Brana is something like 90% WHG and 10% "Magdalenian"? We'll have to check with some stats, but El Miron being already a mix of WHG and "Magdalenian" and having stronger affinity to La-Brana than to other WHGs does suggest that's the case (plus it would explain why La-Brana is more distant from modern populations than other WHGs, without needed exotic ancestry like SSA).

@RK

Yes, I'd like to see some stats with AF3, which they mostly ignore in this paper. It could be that she's similar to MA1 but instead of having an older type of West Eurasian ancestry she had a more WHG-like one. And this would have passed to Native Americans too. I also expect that she will have increased affinity to ENA even compared to Loschbour, but we'll see that.

Shaikorth said...

rk,

That Neanderthal-"basal" relation is an interesting question.

According to this, Turks have less Neanderthal than Europeans which they assume is caused by recent African admixture.
http://meeting.physanth.org/program/2016/session48/taskent-2016-neanderthal-introgression-to-western-asian-human-populations.html

However Sankararaman et al. "Combined Landscape of Denisovan and Neanderthal Ancestry in Present-Day Humans" using the high-coverage Simon's Genome project datasets suggests Greeks, Iraqi Jews, Cretans and Abkhasians, which are not known to have more recent African admixture than Turks (but presumably have lots of "basal"), have even less Neanderthal. There's something going on that won't get truly resolved without Paleolithic Middle Eastern and African genomes

ryukendo kendow said...
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Gioiello said...

If I may say my opinion, it seems that the expansion from the Isles of R1b subclades begins with R-L11: DF100 is overwhelmingly there, beyond a nucleous arond the Baltic and Northern Eastern Alps, but it may be due to the expansion of German people from the Baltic to Crimea, Burgundia etc., but we have in Italy an R1b-DF100 which is an independent haplotype as to the other one that is ancestor of all these German ones, and from R-L23-Z2110-CTS7556 to East as CTS9219, but my brother haplotype Z2110* is 7200 years old as to my Full genome and is now in Tuscany, Basque from France and the Isles. A few are in eastern Europe, for instance Nochev in Bulgary.

ryukendo kendow said...
This comment has been removed by the author.
a said...

@Gioiello

Ha ha ha ha.......Well done! Ha ha ha .....
The bottom feeders are coming out to feed on what is left of their crazy theories, and pride. None of them predicted this result hahaha.Not one.
It is over, I don't think they even realize the position they have to argue their crazy ideas from. This reminds of times past.Remember days with V.V. hahahaha? All your banishment? Anyway, it is much better to keep silent, as it unfolds. Please keep silent.
Now that Italy has two proven basal contenders I-M429+ 30,000+/- years old, and R-M343.IJ-M429+ found at highest frequencies in non speaking Europeans, like proto Afro-Asiatic speaking Arabs and Somalia[Horn Africa]. While on the other hand R-M343+ is almost non existent in those exact same regions, where it comes from, according to your detractors, hahahaha.R1b chose to make a home in the European Italian countryside to Middle East. Please don't respond to any of this, as Trolls are out in full. Just one rhetorical question. Why are people drawn to settle in Italy and Europe?

Shaikorth said...

rk, here

http://genetics.med.harvard.edu/reich/Reich_Lab/Publications_files/2016_CurrentBiology_Sankararaman_DenisovaMap.pdf

Karl_K said...

@a

"R1b chose to make a home in the European Italian countryside to Middle East."

I don't really get the problem here. I never thought it would be unrealistic that R1b carrying men were all over Southern Europe and probably North Africa from very early on.

But the main point is that the huge Bronze Age spread of R1b in Northwest Europe only occurred after it had mixed very well into a Yamnaya-like Indo-European autosomal background.

I wouldn't be surprised if this occurred in Iberia. It even seems likely. It would help explain the lactose-tolerance alleles and R1b in Africa and Italy, and also clarify the non-Indo-European Basque situation.

But the question would still remain about how the Bronze Age people (Bell Beakers probably) ended up with mostly R1b and yet had an autosomal genome so similar to Corded Ware people.

If these R1b branches were actually "native" to western Europe at the start of the Bronze Age, than it is a much more interesting situation than it appeared previously. Somehow these R1b men inherited much of the culture and language and genetics of the R1a steppe people.

Otherwise, the limitations of calling all of the branches of this ancient lineage 'R1b' is a distraction from how distantly related they actually are to each other.

It confuses people.

If we gave each if the star-shaped phylogenies that appeared in the Bronze age a new name, this would be much easier for people to comprehend.

FrankN said...

@Alberto: "We have some 20 samples from Europe from between 40,000-26,000 BP, and none of them is a WHG."
You have overlooked Pavlov 1, mtDNA U5, yDNA C1a2, ~30 kya. If he isn't WHG, La Brana (U5b2c1; C1a2) is neither.

- Then we have from 15,500-14,600 BP 6 Magdalenian samples, who seem to be an extinct type.
That would remain to be tested against current Europeans. In general, Magdalenian mtDNA U8a has survived in Basques, and their yDNA I is still the second most frequent European Hg.

@Rob: "Your position seems to be a bit Italocentric.."
Not really. You may, however, call it Adria-centric, which would include the Western Balkans, and during interstadials connectivity with the Carpathian Basin. Note furthermore that the Late Italic Epigravettian also stretched along the Western Mediterranean coasts, including Sardinia, Southern France and Catalonia, which is essentially where I2a1 is found today (after Sardinia, the next highest concentration is on the Baleares).
Of course, I2 subgroups were quite mobile during the Mesolithic and afterwards. But, with the possible exception of Northern Fennoscandia, there seems to be hardly a part of Europe that has preserved archaic population structure as well as Sardinia. In all likelihood, Sardinian I2a1a still reflects epipaleolithic settlement. This, in combination with our earliest aDNA evidence for I2, namely Bichon (Vilabruna cluster) allows for drawing some conclusions on the I2(a) refugium.

A possible explanation for the success of late/post glacial expansion out of the Adriatic region is described in the following analysis (p. 21) of the Riparo Dalmeri rockshelter, some 30 km W of Vilabruna:
http://www.obermaier-gesellschaft.de/2013_vienna/abstracts.pdf
"The functional study of the macro diagnostic impact traces, has allowed us to recognize different modality of hafting of lithic armatures and (..) largely confirmed the utilization of bow and composite projectiles in the Epigravettian techno-complex, suggesting
moreover a shift in the modality of hafting and association of lithic armatures at the end of the Alleröd. The changing pattern of hunting projectiles, aimed at a more rapid production and an equally quick retooling practice, seems to be tied to an increasing use of the bow and to hunting practices less structured in the territory, involving the frequent loss of projectiles."

Bow and arrow have been (re-)invented several times, this (plus contemporary finds from Sicily) seems to open the European Epipaleolithic story. That story sets forth with Bichon (13.6 kya), who died from a hunting accident, buried below a bear in whose skeleton an arrowhead was found. The earliest finds of complete arrows date to the Ahrensburgian at the eponymous site, ca. 12.6 kya. Use of bow and arrow is a major distinguishing element of Ahrensburgian vis-a-vis the preceding Hamburgian culture.

Kristiina said...

As for yDNA C, in the Palaeolithic Europe we have yDNA C1a (GoyetQ116 C1a Aurignacian, La Brana and Pavlov C1a2) and C1b (Kostenki14 C1b). According to yfull, C1a formed c. 48000 years ago. Today C1a is found (only?) in Europe and Japan, while C1b is much more widespread, covering Australian, Indonesian and Indian yDNA C1. MtDNA of Goyet C1a is M. I would presume that C1a and C1b took a different route to Europe and were autosomally different. If I remember correctly, Kostenki was described to be a kind of an Australoid.

As for the origin of WHG, have a look at the Ice Age vegetation map (https://en.wikipedia.org/wiki/Last_Glacial_Maximum#/media/File:Last_glacial_vegetation_map.pn)
The Near East was mostly tropical extreme desert. The hospitable areas were:
Iberian refuge
Italian refuge
Eastern Mediterranean refuge covering the Balkans and Turkey
Maghreb area
Ethiopia
I think that it is important that there was no barrier between Greece and Turkey, so people could easily move to both directions, so I would say that there is no need to draw a barrier between Eastern Mediterraneans and Near Easterners here. Basal is problematic. During the Ice Age maximum isolated pockets existed in Northwest Africa and the Horn of Africa. I would imagine WHG to be a mixture between European upper Palaeolithic inhabitants and Near Eastern Palaeolithic inhabitants. Maybe Basal came from Africa. We know that there was a cultural and population boom in Northern Africa c. 8000 BC to 6000 BC.

@ruykendo "Alberto and Kristiina, now that we have a sample that is 100% Loschbour-like but further from Han than Loschbour while being no closer to Ust-Ishim, this new dimension 'exposes' Loschbour as ENA-admixed, and therefore locks in some ENA admixture into Mal'ta as well".

Loschbour is only 8000 years old, i.e. he lived c. 6000 BC. microblade technology and pressure technique arrived from Northeast Asia to Europe after the Ice Age and these Siberians surely carried ENA. During Younger Dryas (10700-8200 calBC) these cultures covered Western Siberia and Finland and Baltic area. During Late Boreal – Early Atlantic (7300-5500 calBC), these cultures had spread to Scandinavia. Loschbour's higher Han affinity could be due to the expansion of Siberian microblade cultures to Europe.
Fig. 15 (http://www.quartaer.eu/pdfs/2010/2010_hartz.pdf)

FrankN said...

On the "Basal Eurasian", let me once again suggest the Persian Gulf - mostly dry land until some 8,000 years ago. A prime stopover along the coastal route out of Africa, and, in contrast to most of the Indian subcontinent, far enough away from Lake Toba to offer a reasonable survival chance when that volcano erupted. Reaching the (lesser) Caucasus from there isn't too dificult - just follow Euphrates or Tigris.
Epipaleolithic obsidian trade between the Armenian Plateau/ Lake Van area and Central Mesopotamia is archeologically well documented. It is probably connected to early animal husbandry - summer grazing in the higher mountains, winter in the plains. The Dead Sea and Mesopotamian salt lakes, respectively, of course came in handy to provide the salt required by sheep, goats and (later) cows.

Shaikorth said...

@Kristiina

Kostenki has no particular genetic affinity to South Indian or Southeast Asian or Oceanian populations, that was an old theory based on his bone morphology.

Rob said...

Frank N

Thanks for clarifying. Not much to disagree with then, if we ascribe the phenomena to the Epi-Gravettian sensu latu.

Kristiina said...

Shaikorth, I stand corrected, but my point was to pay attention to the branching of C1 to C1a and C1b c. 48 000 years ago. Maybe that branching happened in Central Asia and not in the Near East as C is (nearly) absent from Africa. C1a ended up in Europe and Japan while C1b prevailed in the south and reached Australia very soon and seems to have disappeared from Europe. According to yfull, K(xLT) formed 45400 years ago and almost immediately K(xLT) split into XNO and MP. We know that NO was in Siberia 45 000 years ago (and maybe in Romania c. 40 000 years ago (Oase1)) and R in Siberia 24 000 years ago. There clearly was a rapid expansion of modern humans between 50 0000 and 40 000 years ago. It is a pity that we lack all paleolithic yDNA and autosomal reference points from India and Southeast Asia.

epoch2013 said...

@Davidski

"I can analyze them with formal statistics, and promise to do so vigorously in the coming weeks."

The papers extende daat table 6 (The whole paper is available fro david reichs site) has a number of D-stats with these ice age genomes in the form of D(Han, Test; French, Mbuti). It may be interesting to see if the patterns visible there are repeated by using other Europeans. Dutch of Lower Saxony Germans, as these are areas within the Ertebolla/Swifterband area relatively untouched by the Germanic migrations. Sweden, as it looks like no SHG admixture is among these. Baltic, as it looks like these were a WHG refuge and Bosnians, as they are I2a rich people with a possible high WHG.

epoch2013 said...

@Matt

"For the Vestonice "Gravettian" cluster it's even worse, since they don't seem to contribute to Villabruna or even El Miron at all."

The paper says it didn't find any conclusive evidence for what three founding populations of Villabrunna were, although they have hints. Table 5.6 in de supplementary info shows D(Goyet116-1, Vestonice16; Villabruna_Cluster, Mbuti) Z=-3.5. Vestonice16 shows in more D-stats *some* affinity with Villabrunna.

Davidski said...

I'm putting together a couple of datasets now. It really depends on marker overlaps. Don't know about Dutch and Swedes yet, but definitely Norwegians and Lithuanians. Bosnians are almost southern Euros, so they won't produce any spectacular stats in this context. I should be up and running tomorrow.

Kristiina said...

I read the Wikipedia article on Natufian Culture and, in particular, "Precursors and associated cultures". Natufian Culture is dated 12500-9500 BC and its precursors fit Satsurblia's timeframe. There are clear indications that Natufian Culture and its precursors had links to Africa, and we should also take note of the Afro-Asiatic language family and its distribution. We even have a suitable yDNA for this Afro-Asiatic gene flow: yDNA E-P147 which is even very frequent in certain areas of Europe. This gene flow should have its counterpart in genetic terms.

Karl_K said...

@Kristiina

I wouldn't be so sure about a genetic link between these cultures.

However, all evidence points to the Basal Eurasians being near the Fertile Crescent and/or Northern Africa and having a long history of semi-sedentary living based on a pre-farming lifestyle.

Excesses of wild plants and animals were collected and preserved and stockpiled whenever they became available.

Eventually they started protecting their food supply well before the harvest.

At some point, the actual domestication of the food supply led to a population explosion and expansion.

I would guess that the genetic link between all of the early farmers and herders is the Basal Eurasian component.

FrankN said...

@Epoch: Thx for the reference to David Reich's side.

After looking at the main paper, a few more takeaways:

1. "We also find that the ~33,000-year-old Muierii2 from
Romania carries a basal version of haplogroup U6, in agreement
with the hypothesis that the presence of derived versions of this
haplogroup in North Africans today is due to back-migration from
western Eurasia."
Interesting.

2."GoyetQ116-1 derives from a different deep branch of the European founder population than the Věstonice Cluster (..)GoyetQ116-1 is chronologically associated with the Aurignacian cultural complex. Thus, the subsequent spread of the Věstonice Cluster shows that the diffusion of the Gravettian cultural complex was mediated at least in part by population movements."

3. Visual inspection of Fig.3 indicates that the Vilabruna cluster has been compiled somewhat arbitrarily. La Brana, and Bockstein and Ofnet (both mtDNA U5b1d1) are all quite distant from the remaining cluster members. Motala12 is hardly further distant than the a/m, and in the PCA clearly clusters with Ofnet and Bockstein, so I wonder why it hasnt been included into the Villabruna cluster as well. C.f., e.g., from Tab S5.6/7

D(Motala12,La Brana; Chaudardes,Mbuti) Z=-4.6
D(Ko1,La Brana; Chaudardes,Mbuti) Z=-3.4

Karl_K said...

@FrankN

"1. "We also find that the ~33,000-year-old Muierii2 from
Romania carries a basal version of haplogroup U6, in agreement
with the hypothesis that the presence of derived versions of this
haplogroup in North Africans today is due to back-migration from
western Eurasia." Interesting."

Very interesting. People have been ignoring North Africa for a while.

Chad Rohlfsen said...

I have a feeling WHG is a mix of GoyetQ, AfontovaGora, and something well "West" of WHG, from West Asia.

epoch2013 said...

@Shaikorth

WRT the differences in Neanderthal admixtures. Could this be misinterpreted as an AMH admixture? Say, something that would be misinterpreted as BE?

@Chad and RK

Take a look at figure 4b: All WHG that show elevated East-Asian affinity also show elevated American affinity. That does look like ANE admixture. Unlike Goyet116-1, which also shows elevated East-Asian affinity - ignored in the paper, maybe considered noise due to age - but no elevated American affinity.

AP said...

Re: “but I would thank here Nirjhar007/parasar, an Indian who exchanged some letters with me on Anthrogenica and elsewhere, even though I said always to him that Indian Indo-European R1a weren't born in India, as you believed and hoped, but came from the Russian plain"

Gioiello,

I don't know if you are conflating Nirjhar007 with me (parasar), but just to clarify: my thinking until the MA1/ANE discovery used to be that R1a-M417 was born close to the North Sea and then moved SE to India with Z93 born somewhere along the way.

Regards.

Arch Hades said...

,"If you look at tree modelling they arrive at WHG being a mix of predominantly new invading population and older survivors related to Goyet and Iberian refugium.
This would explain why ENFs can be modeled as WHG plus something else as they have absorbed WHG-related West Asian group on their way across Middle East to Europe."


As far as I know, ENFs in central Europe or Iberia are just modeled as 10% WHG and 90% Anatolian/Aegean farmer. We don't know what the Anatolian farmers can be modeled as because we don't have Neolithic genomes of the Levant yet.

Gioiello said...

Ok, all clarified, in fact Nirjhar007 said not being parasar and I apologized with him, and with you too now. You know that I have no access to Anthrogenica after they banned me and I lost a little the contacts.

terryt said...

@ Kristiina:

"I would presume that C1a and C1b took a different route to Europe and were autosomally different".

Almost certainly so. In fact likely C1a north of the Tibetan Plateau and C1b south of it. Because:

"my point was to pay attention to the branching of C1 to C1a and C1b c. 48 000 years ago. Maybe that branching happened in Central Asia and not in the Near East"

I suspect the branching is even further east. C1b, as you say, covers Australian, Indonesian and Indian yDNA C1. The really interesting aspect of C1b is that the geographic boundary between C1b1 and C1b2 is Wallace's Line, with the former forming separate branches within Borneo and South Asia, and the latter separate branches in Wallacea and Australia. To me that indicates a split in C1b in SE Asia and presumably a split between C1a and C1b further north in East Asia. And the split between C1 and C2 probably also in the latter region.

Grey said...

"let me once again suggest the Persian Gulf - mostly dry land until some 8,000 years ago"

I read somewhere once that wetlands make for the highest HG pop density and if you imagine where all the wetlands would be in the LGM then I imagine most would be those parts that later flooded
- adriatic
- aegean
- doggerland
- persian gulf
etc

so maybe most of the human population at the time was in those scattered spots - which is a shame as all the evidence would be underwater now.

If true one thing about that which i hadn't thought about before is they'd all have a flood story so not surprising it's common.

Simon_W said...

@Gioiello

I disagree with you about DNA.land, I don't think it's that bad. Their new autosomal ancestry analysis does have its shortcomings and flaws and it's not the best thing available, but I still find it a useful complement. Just one that has to be taken with great caution. The component they call "Mediterranean Islander" is based on samples from Sicily, Malta and Cyprus, hence its name makes perfect sense, even though it does have a strong presence in many mainland Italians as well. (Some other components have been given much more idiotic names.)

Gioiello said...

Simon_W[iesenthal?]
I should write a long letter for explaining all my thought and the tests I am waiting for about many Y and mt lines, but I am tired. Another time I quoted a letter to my friend Dartraighe, and the same I do now. Who wants to understand...

Dartraighe, I am following, even though on the only Activity Streaming, i.e. only the first line, all what the same Celtjews say on Anthrogenica, the blog sponsored and owned from the criminal firm.
You, as an Irish man, know very well the English democracy. What to say? They all have been defeated from me (all the leftists of Stanford and their illustrious Jewish scholars). I have explained many times what happened.
We don't know if Villabruna man is our ancestor, but very likely he belonged to that close tribe of R1b1a from which only one man survived, the R-P297*, who is the ancestor of we all R1b1a subclades.
My hope is that all his descendants understand which is their origin... and in the Italian Refugium there wasn't only R1b1a.
I am waiting that the aDNA is published and they all will know what does mean to be a descendant of the Villabruna clan as I am.

Simon_W said...

Lol, Celtjews... FYI, the W in my nickname stands for Waldmeier, and I wasn't saying this from a Jewish perspective. (According to 23andme I've got 0.1% Ashkenazi admixture - not something that can influence one's perspective and perception of identity, even if real.) I do find antisemitic attitudes silly, but that's even more off-topic than my original comment, so I'll stop it here.

Unknown said...

Ryukendo kendow which WHG specimen exactly doesn't show this Han pull?
A majority if not all of WHGs indeed seem to be ANE/Siberian-like ENA admixed and/or east asian admixed.
http://www.molgen.org/eng/viewtopic.php?f=3&t=2119&sid=a257a5737ccd35de6154f51f00cc0cb7

The type of basal eurasian in Kostenki can be some kind of protoaustraloid thst's why it doesn't increase the distance to Ust'Ishim, however the type of basal eurasian in K14 does seem to have some distant relation to the type of basal eurasian in CHG/Iranian neolithic but not the one in bedouin/ENF/EEF.
Existence of multiple types of basal eurasians is supported by extremely diverging phenotypes of CHG and ENF populations. Compare facial features and the amount of body hair of predominantly ENF Yemeni Jews, Iraqis and Nagev Bedouins to predominantly CHG Boloch, Iranians and Turks.