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Thursday, January 25, 2018

Unadmixed Basal Eurasians lived throughout the Near East ~45-15 KYA?


Below is a map from a recent review paper at Trends in Genetics by Melinda A. Yang and Qiaomei Fu titled Insights into Modern Human Prehistory Using Ancient Genomes.


It's somewhat speculative and an abstract of geographic realities (note that the ancient "Karelia" population is placed several thousand miles east of Karelia, in Northern Asia as opposed to Northeastern Europe). Nevertheless, the fact that the authors chose to illustrate the home of the so called Basal Eurasians as a rather large range in the middle of the Near East, rather than something more remote and limited, like, say, a small part of the Arabian Peninsula or even North Africa, is interesting.

Indeed, they seem to suggest that post-Basal Eurasian Near Eastern populations took shape not as a result of the expansion of Basal Eurasians across the Near East, but rather due the migration of northern foragers (labeled EUR on the map) from Eastern Europe to the Near East. Like I say, no doubt this is based on some guesswork, and needs to be confirmed with more sampling from the ancient Near East, but still noteworthy that it made it onto the map.

Citation...

Melinda A. Yang and Qiaomei Fu, Insights into Modern Human Prehistory Using Ancient Genomes, https://doi.org/10.1016/j.tig.2017.11.008

See also...

Villabruna cluster =/= Near Eastern migrants

116 comments:

Colin Welling said...

Finally, a direct answer to the question of who Mal'ta is more related to, Europeans or Modern Asians.

"First, sampling of Siberian individuals from ∼24–17 ka from the Lake Baikal region (i.e., Mal’ta 1 and Afontova Gora 3) showed that they share a stronger connection to Europeans than to Asians, but that they share the strongest connection to Native Americans"

Karl_K said...

It makes sense, as the Eurasian groups must have been quite diverged before the known admixture events, and all of the groups involved lived in different locations bordering the region on the map, and had very little interaction otherwise.

So there must have been multiple distinct Basal Eurasian populations, all in the vicinity of the Near East, around 15,000 years ago.

Whether they just moved in from North or Northeast Africa, or had already been in the Near East for 30,000 years already?

Anyone's guess at this point.

Shahanshah of Persia said...

Thanks for this David, another excellent post on your part.

Bob Floy said...

So this would be a handy explanation for how Barcin, for example, got all of that WHG?

Davidski said...

@Bob Floy

So this would be a handy explanation for how Barcin, for example, got all of that WHG?

Something WHG-related; probably from the southern Balkans. And Boncuklu had even more...

http://eurogenes.blogspot.com/2016/08/pca-analysis-neolithic-central.html

mickeydodds1 said...

'Everyone is eastern European' ;)

Aram said...

Uniparental markers never favoired the idea that BE came from Arabia or yet alone from North Africa. One needs to extrapolate the existing data about y dna G, J, T, L, E-m35 to understand that BE was in central parts of Near East since very long time.

Aram said...

Yes Anatolia was probably the most BE less place in Near East.
Btw BE is as distant from SSA than Goyet and Tinyuan. So it could emerge anywhere in Eurasia but it happened that it emerged in West Asia.

Aram said...

So Villabruna has some EAS?
And who carried that EAS to Europe?

Bob Floy said...

@davidski
Kind of a blunt question, but given the size of BE's territory in this scheme, would you say that this could tell us anything new about the relationship between the Anatolian and Iranian neolithic samples?

Davidski said...

@Bob Floy

Kind of a blunt question, but given the size of BE's territory in this scheme, would you say that this could tell us anything new about the relationship between the Anatolian and Iranian neolithic samples?

No more than my working qpGraph topology for ancient Eurasia, I guess?

http://eurogenes.blogspot.com/2017/07/working-topology-for-eurasian.html

In so far as that all Basal Eurasians were fairly closely related, and what really separates the Anatolian and the Iranian farmers is a lot of input from pWHG into the former.

Bob Floy said...

@davidski
"In so far as that all Basal Eurasians were fairly closely related, and what really separates the Anatolian and the Iranian farmers is a lot of input from pWHG into the former."

This more or less answers my question, thanks.
I've had some difficulty understanding the specifics of the Anatolian/Iranian neolithic divide. Fascinating stuff.

Matt said...

Yeah, they don't really know of course.

Davidski: Indeed, they seem to suggest that post-Basal Eurasian Near Eastern populations took shape not as a result of the expansion of Basal Eurasians across the Near East, but rather due the migration of northern foragers (labeled EUR on the map) from Eastern Europe to the Near East.

Assuming their model, I suppose there are reasons to think that the European forager populations may have moved around a bit more - glaciation. The European forager zone (just as a quick term for the non-ME West Eurasian zone, without too much thought) is the kind of place that is going to be frequently hit by population crashes due to glaciation, and as climate changes, that will motivate people to migrate (the climate refugees of pre-history?). That may not have been such a salient pressure in the south, and where it was, they surely are not going to migrate north when it happens.

(Much historical models of the peopling of Eurasia tend to think of the more northern regions as supporting smaller less dense populations and so sinks... but they may have had quite large populations when conditions were good and opened up after glaciation, and when conditions were bad, more of a reason to migrate south, despite being less competitive in that zone.)

I think their placing of EAS in the model in 34-15 kya is interesting. Again, no real reason I can see not to place this pop further west or north. That would help with the disjoint stats between Mesolithic and Upper Paleolithic European in relatedness to Han and Tianyuan, which they have in Fig 3 (and the light indigo shading in the east of the VB cluster in Fi 1, though this really should be in the Karelia cluster too, properly). But where the pop is placed also seems pretty viable. (Maybe its a conservative position, or Bhutan, Nepal, Tibet is preferred in the Chinese labs they are working in for cultural reasons...)

Off topic (and operating on about the furthest other end to the scale): The Martiniano paper on the British Isles was published http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1007152 (nice turnaround time...)

Rob said...

“Indeed, they seem to suggest that post-Basal Eurasian Near Eastern populations took shape not as a result of the expansion of Basal Eurasians across the Near East, but rather due the migration of northern foragers (labeled EUR on the map) from Eastern Europe to the Near East.”

I agree . Alberto and I have been saying this for yonks
I even think that hg J was initially “UHG”

Rob said...

The substrate of Palaeolithic Caucasus and Anatolia was UHG (loosely defined). Basal then encoaches upon this Epi Gravettian and Post Aurignacian (resp.) base after the LGM.
There’s a lot more paleo data coming too

Alberto said...

@Rob

Have I really said such thing before? Not sure about that...

It's really a mystery how things went during the UP, and it will be until we get samples from more southern regions. But with the data we have, I'm not so sure about that model of southward migration.

We have many (20 or more) samples from North Eurasia pre-LGM. Looking at the western part (Europe), we have especially many samples from across the continent and long time span. In that model (that Matt has elaborated about), we would see that those pre-LGM Europeans would have gone south and mixed with Basal Eurasians. But we don't really see that. It looks more like those populations basically went extinct when the LGM came (small exception of those Magdalenians that survived a little longer).

And then we see a new population (WHG) colonizing Europe. From where? Not from Europe itself (since we have preceding samples from across the continent) and not from Siberia (we have samples too).

Looking at the eastern part of North Eurasia, we have MA-1 already there before the LGM. In that model of southward migration during cold phases, we could imagine that East Asians (mostly in China) would be a mix of whatever basal East Asian and ANE. But again we don't really see this. Chinese have noise levels of ANE admixture. But Siberians have some 80-90% admixture from East Asians.

So unless further samples really turn this around, it seems to me that migrations have clearly gone south to north. Or is there a different way of looking at the data already available?

Davidski said...

@Alberto

And then we see a new population (WHG) colonizing Europe. From where? Not from Europe itself (since we have preceding samples from across the continent) and not from Siberia (we have samples too).

From Eastern Europe and Western Siberia.

Davidski said...

@Matt

Yeah, they don't really know of course.

They might know.

Rob said...

@ Alberto

Oh yes . I agree- I misread Matt’s statement to mean UHG type groups living in an expanse is SEE to Caucasus and perhaps beyond prior the basal expansion. It’s different to what you suggested - But my elaboration is clear enough, and is essentially what you said


However I wouldn’t discount north to south forager movements either - we have Levantine Aurignacian, the I2c in anatoalia , bullet cores in Anatolia and near east. It has even been suggested that the Anatolian epipaleolithic is northern origin

Kristiina said...

@ Rob

And the mtDNA phylogeny can be interpreted to show an upper palaeolithic migration of mtDNA U from the north to the south and a the migration of mtDNA K from Southeast Europe to Anatolia and Near East maybe just around the glacial maximum.

astenb said...

Is that a typo or does Natufian have more BE than HOTU?

Alberto said...

Yes, some influence of Paleo Europeans in Anatolia to form WHG proper (from UHG) is possible.

@Davidski

We have pre-LGM samples from European Russia (near Ukraine), Romania, West Siberia/Central Asia (Altai)... Not really WHG or UHG.

Davidski said...

@astenb

Natufians have more BE than Hotu, definitely. See here...

https://eurogenes.blogspot.com/2016/07/sneak-peek-basal-eurasian-k7.html

Davidski said...

@Alberto

http://eurogenes.blogspot.com/2016/05/following-mammoth-herds.html

Salden said...

I speculate the Predynastic to Middle Kingdom Egyptians were a largely Basal Eurasian with a ruling caste of Neolithic Iranians. Fitting in line with the Dynastic Race Theory.

Kristiina said...

Kostenki and Sunghir were autosomally very similar and they carried similar haplogroups. Kostenki site is close to the Ukrainian border, but Sunghir is further north in the Vladimir Oblast, east of Moscow.

http://science.sciencemag.org/content/early/2017/10/04/science.aao1807.full

http://generatioaequivoca.blogspot.be/

EastPole said...

David, this is OT but here is short relation of what prof. Grzybowski said yesterday on genetic structure and genetic history of Central Europe (in Polish)

https://s18.postimg.org/bxzkywlft/screenshot_329.png

Davidski said...

@EastPole

Sounds like that talk was based on modern-day DNA though. So unless they have ancient DNA to back up their conclusions, then nothing's certain.

Anonymous said...

@Alberto

"So unless further samples really turn this around, it seems to me that migrations have clearly gone south to north. Or is there a different way of looking at the data already available?"

We entirely miss an important sample form Ice Age Europa: Solutreans. Also, the Red Lady el Miron carried part WHG *and* showed that mysterious affinity. She also lived almost during the LGM. She doesn't have any Basal admixture.

So you suggest an WHG like population migrated north *during* LGM? Why?

Anonymous said...

@Alberto

That "mysterious affinity" being that affinity to Middle-Easterners.


Mind you, D-stat show that it is an affinity to Natufians, to Anatolian Neolithics, to Iran Chalcolithic but hardly to Iranian neolithic.

Mbuti Levant_Neolithic Kostenki14 Villabruna 0.0464 8.951 710555
Mbuti Levant_Neolithic Kostenki14 Bichon 0.0310 5.932 806519

That is about what Fu et al has with Iraqi_Jew.

Mbuti Iraqi_Jew K14 Villabruna 0.0038 7.8 1125277
Mbuti Iraqi_Jew K14 Bichon 0.0037 7.9 1669947

Iran Neo doesn't

Mbuti Iran_Neolithic Kostenki14 Villabruna 0.0137 2.493 716391
Mbuti Iran_Neolithic Kostenki14 Bichon 0.0156 2.841 823008
Mbuti Iran_Neolithic Kostenki14 Loschbour 0.0113 2.056 815524

Iran Chl does:

Mbuti Iran_ChL Kostenki14 Villabruna 0.0271 6.144 807309
Mbuti Iran_ChL Kostenki14 Bichon 0.0238 5.342 965639
Mbuti Iran_ChL Kostenki14 Loschbour 0.0234 5.421 957873

Alberto said...

@epoch2013

Yes, exactly, El Miron is the earliest sample that has some WHG admixture (~30%?). So it means that WHG entered Europe somewhere around 25-22 Kya?

Why would WHG have such affinity to Natufians, Levant_N and Anatolians? Natufians are some ~50% WHG-like (UHG?). I don't think it's because WHG came from Siberia or Eastern Europe (those are about the only places we can exclude, since we have samples, in fact).

But if you elaborate on how would you interpret the data available, I'm interested in any idea that makes sense.

Rob said...

Solutreans are just going to be something between the Aurignacian and grevattian trees; so they won’t change anything

Alberto, according to the recent Sikora paper, the dolni vestonice sample also has some WHG admixture, much earlier than El Miron
mtDNA U5 also appears in the Dolnis, U5 being the later archetypal lineage of the WHGs

So I think that suggests WHG might already have been arriving in Europe toward the middle UP; just prior the LGM- as a bridge from CE to SEE through to Anatolia, Caucasus etc

Anonymous said...

@Alberto

Consider Kostenki14, GoyetQ116 and Oase1. They are highly different, even if K14 and GoyetQ116 are clearly from the same stock while Oase1 isn't. This might give an indication that ice age people were highly diverse.

Also consider that Magdalenians were partly GoyetQ116. That means that a group of people can "disappear" for 15.000 year from the samples, even if that isn't the case.

Both considerations mean IMHO that we may simply haven't found the key-sample, the key-population to explain WHG. Considering that El Miron had part WHG and had mtDNA U5b, which was considered by Cosimo Posth 2016 to be a marker of the WHG population turn-over she must have been near that key-population. It could have been in Italy as well, as Paglicci71 - also 19k yo - was U5b2b. I tend to hint at the Solutrean, but that is merely because I know it's an unsampled paleolithic culture, even though they practiced pressure flaking according to this post:
http://www.aggsbach.de/2014/10/pressure-flaking/

And they were in the right spot at the right time to provide the admixture.

The relation to the Natufians is unclear. To an amateur such as me it looks old - No Y-DNA I/mtDNA U5 there. Israeli archaeologist Ofer Bar-Yosef once stated that the Levantine Aurignac seems very related to the South of France but is dated *later* than it. Could the spread of mtDNA U6 be related? If we consider such an old link as I do we are relieved of the question where Y-DNA I would be, as it's expansion in paleolithic Europe could be situated much later.

Mind you, this is all highly speculative.

Anonymous said...

@Rob

"Solutreans are just going to be something between the Aurignacian and grevattian trees; so they won’t change anything "

Apart from the fact it's just a suggestion Kale from anthrogenica managed to model Villabruna as 8% ANE and the rest divided as 2/3 El Miron and 1/3 Vestonice. If only I could find the link...

Rob said...

Epoch is sure they’re important for within Europe playing around, i just meant it won’t be an “alien” population, but somewhere along an existing cline

Eren said...

Always interesting to read about Basal Eurasians, even if it's just a review article.

In the context of the above discussion regarding north-to-south vs south-to-north movements, the fossil record of the Levant (or Israel to be more specific) seems to rather support a south-to-north movement of Basal Eurasians. Fossils from the late Upper Paleolithic time period (27-19 ky BP) seem to be of the Cro Magnon type. The youngest of those remains is from the site of Ohalo, which includes a complete male skeleton (Ohalo H1). Here is a picture of his skull (the one at the bottom): https://static.cambridge.org/resource/id/urn:cambridge.org:id:binary:20170503114805377-0842:9781316106754:09046fig68_2.png

I'd bet we are looking at a representative of the so called "UHG" here. The skull at the top is from Nahal Ein Gev I (27-25 ky BP), a female specimen from the same anthropological cluster.

"From the anthropological perspective, therefore, there is no clear association between the late Mousterian/Initial Upper Palaeolithic periods (Manot) human populations and later (<30 ka) Upper Palaeolithic populations in the Levant (e.g. Qafzeh). The former is associated with early Upper Palaeolithic central European populations (e.g. Mladec) bearing many archaic traits, whereas the later are more of the Cro-Magnon type. This may imply population movements in and out of the southern Levant from/to western Asia, Europe, and Africa during the Upper Palaeolithic."
(Hershkovitz & Arensburg 2017: 612-613)

Starting with the Kebaran the divergent Natufian type emerges in the fossil record. These specimen are rather heterogenous, with some showing more continuity with the Cro Magnon types (e.g. Eynan) and other much more archaic (e.g. Hayonim cave). A skull comparison here: https://static.cambridge.org/resource/id/urn:cambridge.org:id:binary:20170503114805377-0842:9781316106754:09046fig68_3.png

Eynan specimens were also taller: "average male stature at Eynan was 174 cm tall and females 162 cm, whereas in other Natufian sites (Hayonim Cave, Nahal Oren, el-Wad), males were <170 cm tall and females <160 cm." (Hershkovitz & Arensburg 2017: 616)

Seems to me that Basal Eurasian admixture into the Levant is not older than the Kebaran, which is also why Natufians show such heterogeneity. Similar, but less significant morphological differences are observed in the Iran Hotu specimens. A mixture of cold and warm adapted people, some leaning more towards the one or the other. Admixture events that hadn't had the time to produce homogenous blends at that point in time.

Anonymous said...

@Rob

That could indeed be the case. Than what we call WHG is basically a mixture between Aurignacian and Gravettian and the difference between Magdalenian en Epigravettian is merely the ratio. Considering that the Ahmerian is sometimes associated with the Gravettian and was contemporary to the Levantine Aurignacian, IIRC, than the WHG admixture in Natufians should be more or less an accidental similar ratio.

Does this fly?

OTOH the Solutrean is a really different culture if I understood everything I read correctly.

Do you if there was a link between Solutrean and the Swiderian? I read the latter had willow leaf blades.

Samuel Andrews said...

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http://mtdnawiki.com/order-an-mtdna-report-6/

Lee Albee said...

It is interesting that the appearance of the BE genetics roughly coincides with the flooding of the persian gulf basin (http://people.rses.anu.edu.au/lambeck_k/pdf/171.pdf).

An area that was relatively isolated by hyper-arid zones and mountains to the North. Suspected to be an inhabited area from possibly back to 100K years ago. http://www.jstor.org/stable/pdf/10.1086/657397.pdf.

So a BE population homeland may have centered in the gulf region. With later exansion into the fertile crescent and Zargos .

The map in this paper seems to overlap the gulf anyway.

Lee

Greg Dahlman said...

Related to the notes about Ust-Ishim and this paper and to help with my own ignorance.

Noted that this is small segments and that I am in no way making a claim of relatedness, or validity of the tools.

But I see that this claim is often made as it is in this paper.

"Not represented in populations today, used to date Neanderthal admixture."

Yet according to Gedmatch I have:

Largest segment = 4.9 cM
Total of segments > 1 cM = 800.5 cM
483 matching segments

Which is actually a bit closer than I am with most random available stranger data (also anecdotal, biased and non-scientific)

While it may just be a function of the segments that were tested and chance why is it assumed that Ust-Ishim is not represented in populations today?

yes 1 cM segments are short, but 800.5 cM for such an old sample seems like a lot to me.

Rob said...

Epoch

No it does not fly because WHG isn’t from the solutrean, that’s your misconception

Samuel Andrews said...

@Shah,

I found a young EEF lineage shared exclusively between eastern Europe and SC Asia (including India and other Indo-Aryans).

Anonymous said...

@Rob

"No it does not fly because WHG isn’t from the solutrean, that’s your misconception"

Why is WHG not from Solutrean?

But indeed it won't fly because it would require that other Ice Age Europeans than El_Miron and WHG als would show an affinity to the Middle East and they don't - not even GoyetQ116! - as the D-stats in Fu et al show.

But that limitation makes the case for an unsampled population. Mind you the fact that GoyetQ116 does not show that affinity tells us that the affinity must be related to the WHG part of El Miron.

Anonymous said...

@Greg Dahlman

Ust'Ishim came from permafrost and has an exceptionally well preserved DNA. That may explain it.

Anonymous said...

The odd thing with placing BE's in Arabia is that either the split between them and the rest of the Eurasians needs to have occurred there, or the expanding HG's out of Africa that formed the paleolithic Eurasians must have managed to do so without getting in touch with BE's.

Eren said...

Regarding the BE estimates in the paper: "Basal Eurasian ancestry is highest in the Near East, with estimates as high as 66% in Epipaleolithic Natufian individuals from the Levant ∼12–9.8 ka, and 44% in a Mesolithic individual from Iran from ∼9.1 to 8.6 ka (i.e., Hotu)."

At first I thought these were new estimates, confirming what some (incl. Davidski) have here been saying (Natufians being the most basal). But they actually refer to Lazaridis et al 2016. So, they must have switched up the numbers as Lazaridis has them the other way around.

Alberto said...

@Rob

Yes, the details are of course very blurry, and we'll need further samples to really know if and how much Paleo Europeans contributed to WHG, where and when.

But I think that the general picture from the data is quite constrained to change too much.

@epoch2013

It could be a matter of bad luck. But again this is about probabilities rather than about what's just possible. Imagine that we know about this shared ancestry between West Asians and LUP/Mesolithic Europeans, so we'd have 2 competing hypotheses: Either a West Asian population moved to Europe or a European population moved to West Asia. And in principle (ignoring everything else), we could give each one 50/50 chances.

So then we try to get genomes from 40-25 Kya to see which one is correct. But due to climatic conditions (among other factors), we manage to get 20+ samples from Europe and none from West Asia. And it turns out that none of the 20 samples from Europe from that period are WHG. Would that increase or rather dramatically decrease the chances of a European origin? I think the latter. Saying that the right samples have been missed by chance is going for the least likely scenario.

But add more constraints to that:

- You'd need that missing population not just to colonize all of Europe, but to venture deep into West Asia (including Arabian peninsula) and North Africa. That's quite an expansion for a hidden population from Europe.

- And on the other hand you'd need that those Basal Eurasians (unadmixed), who branched off from the rest of Eurasians some 70 Kya would be in West Asia since then and never ventured into Europe until some 9 Kya (and never to East Asia). Is that a plausible scenario? And where was Europe being populated (repeatedly) then, if West Asia was occupied by Basal Eurasians?

Anonymous said...

In the first map, I would safely connected from Ust-Ishim to Oase, and probably to the Tianyuan.


And shows areas of Basal Eurasian do people generally live? People lived in Palestine.


On the second map why they did not join Sunghir and Central Europe? Scared of what? Anthropologically they belonged to a Brun-Prsedmost type.

The third card I agree, the only EUR likely direction was from East to West.

Mark Moore (Moderator) said...

@Eren,

I am fascinated by the Basal Eurasians. Your observation is particularly interesting":Seems to me that Basal Eurasian admixture into the Levant is not older than the Kebaran.

So are you suggesting that the Kebaran people are in fact the BE? That if we could get DNA on one of them we would find the pure BE DNA? These people seem to come out of nowhere, with no samples of them > 13,500 years ago. Where were they?

Rob said...

@ Epoch

“”WHG “ are a Late Glacial expansion event
That is 10000 Years and 2 admixture events after the Solutrean
So I won’t ruin the surprise on details

Anonymous said...

@Alberto

"You'd need that missing population not just to colonize all of Europe, but to venture deep into West Asia (including Arabian peninsula) and North Africa. That's quite an expansion for a hidden population from Europe."

No, not colonize. Admix.

Europe during Pre- or Proto-Aurignacian had them, next to several others such as Oasis1. Then Phlegraean Eruption, end of Oasis1, the whole area cleared by that eruption is retaken later. That explains the migration to the Middle-East.

"- And on the other hand you'd need that those Basal Eurasians (unadmixed), who branched off from the rest of Eurasians some 70 Kya would be in West Asia since then and never ventured into Europe until some 9 Kya (and never to East Asia). Is that a plausible scenario? And where was Europe being populated (repeatedly) then, if West Asia was occupied by Basal Eurasians?"

But then you state that the Middle-East admixture is basically Basal Eurasian. However, in SI chapter 8 of Fu et al they already make clear there is no Basal Eurasian in pre-neolithic Europeans.

But that's not all. All of the populations resurrecting from LGM went through a bottle-neck. But not in the Middle-East. So, if a migration from the Middle-East is the cause of WHG it had to be pre-LGM. But pre-LGM we don't see anything that matches.

However, if we consider both el Miron and WHG an admixture of several pre-LGM pops, with WHG being GoyetQ116 + Gravettian + our assumed population + a tad ANE and El Miron GoyetQ116 + our assumed population we can account for a lot.

@Rob

”WHG “ are a Late Glacial expansion event
That is 10000 Years and 2 admixture events after the Solutrean


Okay. But I was merely considering Solutrean a part of the mixture.

Matt said...

@David, could be. I almost never want to assume they're holding anything back tho.

@Alberto: So unless further samples really turn this around, it seems to me that migrations have clearly gone south to north. Or is there a different way of looking at the data already available?

So at the moment we have: Villabruna and Bichon (almost simultaneous at 12,000 BCE / 11,700 BCE) and almost simultaneously Satsurblia cave sample and the Natufians.

If we're having a migration from east of the Balkans, then you need a simultaneous migration such that BEu was just arriving in both Satsurblia and Natufians (and so highly likely all the land between them) at exactly the same time the ME HG was leaving for Europe.

That seems like a lower probability event than that Villabruna is (largely) just Balkan Euro HG (since we have no Euro UP HG samples from the region) which shared ancestry with various HG in the Middle East at some point earlier in history (pre-BEu, or maybe one way if BEu was always there)...

(I guess could be isolated Anatolian, but I believe that the idea is that this area was depopulated in the late Upper Paleolithic? In any case, the Levant and Mesopotamia seem out).

(In a general sense, of course we have fairly plentiful examples of geneflow going north (cooler) ->south (warmer) through history as well. SE Asia obviously has ancestry out of China, the IAM people from North Africa don't really exist any more, India (one way or another), East Africa, multiple migrations into North America by waves of Native Americans with varying levels of relatedness to present day Siberians, modern day Caucasians are certainly far less BEu, or at any rate, more affected by EHG, than the ancient Caucasus of Satsurblia and Kotias, etc.

The Balkans to the Levant is a mere hop and a skip away by comparison...)).

Looking at the eastern part of North Eurasia, we have MA-1 already there before the LGM.

Hmmm... I wonder about that. How much do we know about what happened there? We know that Native Americans of some sort existed likely in Beringia, but I wonder how much they had been marginalised by Devil's Gate types (who evolved god knows where) in much of the rest of Eastern Asia before that...? (Perhaps by multiple layers of ANE->East Asia migration until little autosomal trace was left).

(The paper on Baikal Hunter Gatherers may be an interesting game changer here "Our genome data (~1X) reveal that Baikal Hunter-Gatherers (BHG) are an uncharacterized genetically homogeneous branch of Inner Asian hunter-gatherers, displaying highest shared genetic drift with present-day East Asians. Targeted sampling strategies coupled to excellent biomolecule preservation has permitted the generation of an advantageous sample size dataset (n = 31), rendering possible to estimate allele frequencies within these groups, thereby optimizing population tests. BHG model as an excellent proxy for an Inner Asian source population admixing into the late Bronze Age Andronovo groups, becoming Iron Age steppe nomads." https://twitter.com/amwkim/status/848304278607249408 It may turn out a major migration of BHG to the south really did hit during the LGM.).

Though I'd also say my toy model does imply frequent population crashes and extinctions as the consequence for populations which do not successfully migrate... Where are the Vestonice cluster? Quite possibly nowhere really.

Anonymous said...

@Matt

"Though I'd also say my toy model does imply frequent population crashes and extinctions as the consequence for populations which do not successfully migrate... Where are the Vestonice cluster? Quite possibly nowhere really."

But we see that populations that completely vanish from the radar resurrect 15.000 year later: GoyetQ116 -> Magdalenians. That doesn't feel like extinctions were the norm.

Matt said...

Btw, thinking again about those Han+Tianyuan assymetries in Figure 2...
Seems like you need a functional trifurcation of (Tianyuan)(West Eurasian)(Other Han Related ancestry) lineages to get the model.

The later Villabruna cluster members are getting some ancestry X which makes them closer to Han... but not closer to Tianyuan, compared to previous UP people. So this cannot be ancestry which shared any significant degree of drift with the Tianyuan clade relative to what the rest of the West Eurasian (K14 related) clade had.

But at the same time, X cannot share any drift with West Eurasian, or Han would be closer to K14, etc. than Tianyuan (which is not the case).
So seems like East Eurasians have to be descended from at least 2 deeply diverged lineages, (one of which is Tianyuan related), which are effectively part of a trifurcation with West Eurasian (don't get too hung up on the labels).

Oase1 and Ust-Ishim show us that such populations existed, effectively at a trifurcation (some do show evidence that they shallowly can be fit on the West Eurasian / East Eurasian parts of a tree, but they are effectively trifurcated in how weak the stats are).

I'm guessing this is what is meant by "complex population split" between West and East Eurasians...

Assuming this works, at some point you'll find a population that shares almost no more ancestry with Tianyuan than with K14... But lots more ancestry with Bichon than Villabruna and K14 and lots more ancestry with Han than Tianyuan.

Anthro Survey said...

Lee beat me to the article, but, yes, that is also how I see things unfolding.

I wonder, though, if there were actually two basal populations in the past: either with one being more basal to the other OR both being divergent clades of the same early split.

At any rate, I envision one as an early back-to-Africa, E-carrying lineage and somewhat important for Natufians. The other I see as having been more important for early Neolithic Iran, Boncuklu, and (unsampled) northern Mesopotamia. Predominantly Y lineage CF.

Do formal methods reject such scenario(s)?

Anonymous said...

They have maps under EUR refers to quite different sizes. The third map EUR they have EHG. Karelia is EHG. And the influence was clearly from East to West, and not back. A third card can not be interpreted otherwise. No arrows from where they portrayed EUR to the place where they portrayed Karelia was not. There was an arrow in the opposite direction. In General, the map certainly full of noodles, in order to forge the concept they have even portrayed Europe and Karelia with one color.
EHG and WHG come from different sources.

Anthro Survey said...

@David

Looks like the Guanche genomes are available. When do you think you'll be able to add them to your datasheets?

Will have to wait for the Early Neolithic Moroccans to come in, though. Should be interesting to run formal stats on those.

a said...

Any possibility to make a pca with WHG-EHG-Basal Eurasian-Neaderthal-Denisova- Chimpanzee?

Anonymous said...

Matt
"The later Villabruna cluster members are getting some ancestry X which makes them closer to Han... but not closer to Tianyuan, compared to previous UP people."

See Figure 2 C Karelia this paper
and https://eurogenes.blogspot.com/2018/01/the-kho-people-archaic-indo-aryans.html?showComment=1516961462272#c693211402176772967

This people probably was closer to AG2. He walked to West trough Sunghir-like population.





Chad Rohlfsen said...

Rather than WHG being some odd pop that minimally mixes into Vestonice and ElMiron, it is more likely that Vestonice is closer to the branch WHG came from, so they share minimally more drift and ElMiron is probably mostly WHG.

Matt said...

@Davidski, a couple of test qpGraphs for my idea on a trifurcation of populations explaining the differences in relatedness to Han vs Tianyuan among Villabruna clade pops:

1: https://pastebin.com/14ZrVnqn
2: https://pastebin.com/pqfEh2yx

If you could possibly run them, I'd appreciate it.

Unknown said...

I find it pretty amusing that a site with the title Eurogenes is attempting to use y-chrom genetics to support the aryan invasion hypothesis.

Here's my deal. I'm genetically western european. Politically I am neither repugnantcan or demoncrap, but lately more conservative...I informed myself about Killary's criminal activities, LOL.

Philosophically, Spiritually I am advaitin/ pre-hindu.

Education - I was a molecular biologist.

I can GUARANTEE YOU and any uninformed reader that chronology is a big issue with your sample size and limited genetic data. Your conclusions in terms of migration, and definitely "invasion" are speculative at best, as you ignore the fact that there is no precedent for the culture/philosophy/religion of ancient India, and no evidence for it in western culture at any time.

The idea that europeans brought Sanskrit, gimme a break. Vedic and pre-vedic culture was advanced when Sumerians were non-existant.

Bob Floy said...

"Vedic and pre-vedic culture was advanced when Sumerians were non-existant."

Did they ride around on Unicorns?

Davidski said...

@Unknown

It's nice to hear that you're amused. But when you manage to find some time away from giggling and whatnot, you should change your nick to Clueless. At least then other people here would know what to expect when you decide to take up bandwidth with your comments.

Obviously, the idea that DNA can track expansions of languages, and especially Indo-Iranian and Indo-Aryan, is taken very seriously by a lot of people, because it's supported by solid evidence and strong arguments.

And if you want to challenge this idea, particularly in the case of Indo-Iranian, then you actually need to take some time to learn about the said evidence and arguments, and come up with coherent counter-arguments, and not just a few irreverent personal thoughts on the topic.

For instance, how do you explain the close and relatively recent linguistic, Y-chromosome and genome-wide relationship between Indo-Aryans and Balto-Slavs?

These groups, often classified by historical linguists as linguist sister clades, live many thousands of miles apart, yet they share the Y-DNA R1a(Z645+) mutation, which expanded across much of Eurasia during the Bronze Age, a time frame also associated with the expansion of Indo-European languages.

So what do you say to that? Do you have a more plausible explanation for it than the expansions of the ancestors of both Balto-Slavs and Indo-Iranians from a common ancestral population in Eastern Europe, where, for instance, ancient DNA has shown the presence of the chain of mutations leading to Balto-Slavic- and Indo-Iranian-specific clades of R1a?

Feel free to dazzle us with your scientific mind.

@Matt

Your qpGraph trees...

https://drive.google.com/file/d/162quJ-m9aeyGtPyyJV9VWmObmKUjWvIr/view?usp=sharing

https://drive.google.com/file/d/1YoVJL0-6pPTkbkOy0-UkK4l_iAtk-hYc/view?usp=sharing

Rob said...

Anthro
The structure of E shows it emerges from Africa, not into it . This is couples with Archaeological evidence of movement from Africa to Near East c 25 ooo yBp

Greg Dahlman said...

@epoch2013

Thank you as I had missed the massive difference in coverage.

GedMatch abstracts that metric away. It looks like I will need to start working with the raw data. It may not result in better data but at least I will know the source of all errors (me).

Rob said...

@ Matt
About Han, & picking up from months ago, the recent “Scandinavia” paper clears that up no ?
There signifixant EHG shift in Norway, along with which came Han affinities down the Atlantic to LB. (?)

Anthro Survey said...

@Rob

You believe DE split in Africa? Unlikely to have been too deep inside Africa considering the absence of D there.

As for the movements from Northeast Africa into the Levant----do you think they were coupled with SSA lineages, or, as I suggest, with a ghost lineage basal to other OOAs but "crown" in relation to SSA lineages?

If the latter was, indeed, the case, Natufians and modern Bedouins probably get most of it in the Near East. Perhaps Harifians and pre/early Dynastic Egyptians as well.

Also curious: Where do you place the AA urheimat?

Ryan said...

You would think Basal Eurasian had to be intrusive at some point in order to lack Neanderthal ancestry. I guess that movement was pretty old though.

Can you get treemix to more or less capture this?

Also Qiaomei Fu is a rockstar.

Davidski said...

@Ryan

Can you get treemix to more or less capture this?

Which part?

But I've swapped TreeMix for qpGraph, because there's generally much less fiddling around.

Rob said...

@ Anthro

No I think DE is Eurasian, at face value at least. However, having a TMRCA of 63ky BP, it's not particularly relevant to Natufians and the LGM.

So if DE back-migrated to Africa, E still grew and diversified in NE Africa (or wherever specifically). It seems the Nile region was a significantly densley settled refuge during the LGM, which then became depopulated during the Final Paleolithic, which is broadly when the Natufian industries, and their ~ E-M35 lineages appear.


And I think if there were the movements from N Africa to ME, they'd lack SSA. (But I profess no expertise in hg E)


About AA - similarly I don't know that much about it, but the cladistic tree suggests a movement from E Africa also ? What I find more interesting is the origin of Semitic, the role of intrusive patriarchal highland J clans, and possible analogies/ lessons for Indo-Hittite.

Anthro Survey said...

@Rob

"So if DE back-migrated to Africa, E still grew and diversified in NE Africa"
Ok, this is my thinking exactly. So, no disagreement there.
I'm just really curious about the autosomal nature of this possible back-migrant ancestry and its ultimate role in Natufians'/IAM pseudo-SSA shift.

Based on my limited knowledge of prehistoric NA/Levant, it really does seem that in certain periods of late paleo and mesolithic, Egypt was a densely populated region and a genetic source for outward migrations---into the Levant and westward into the Maghreb.
e.g. Fayuum culture has ties to Harifians; Motif similarities between Iberomaurisian, Egyptian and Levantine industries, etc.

The J founder effect w/respect to Semitic languages is interesting since frequency of J in Arabia is really disproportionate to 'West Asian highlander' ancestry. I subscribe to the circum-Arabian hypothesis, atm:

The 'Akkadian' branch seems straightforward. Initially migrated northward, hybridized with local ANF-CHG people and then followed the Tigris/Euphrates down to the Gulf.
As for south Semitic, I suppose there was also a mixing stage in the Levantine hinterland during which they acquired J and carried it south through the Hijaz(and ultimately to the Horn).

MomOfZoha said...

@David:
"Indeed, they seem to suggest that post-Basal Eurasian Near Eastern populations took shape not as a result of the expansion of Basal Eurasians across the Near East, but rather due the migration of northern foragers (labeled EUR on the map) from Eastern Europe to the Near East."

Regardless of the arrows in that picture (which clearly does not represent any complete picture), the authors were careful not to make such a claim/implication in the text.

From the paper:
" In the Caucasus, ∼13–10 000-year-old individuals (i.e., Satsurblia and Kotias) show a close relationship to ancient individuals in West Eurasia, but they also possess the Basal Eurasian ancestry observed in populations from Europe and the Near East [13, 27, 28] (Figure 2B). Basal Eurasian ancestry is highest in the Near East, with estimates as high as 66% in Epipaleolithic Natufian individuals from the Levant ∼12–9.8 ka, and 44% in a Mesolithic individual from Iran from ∼9.1 to 8.6 ka (i.e., Hotu) [28]. Further sampling will help to determine whether the gene flow between populations in the AMC began during this time period or extends back into the AMB.

Regardless of the timing of gene flow between East and West Eurasia, some amount of either Near Eastern ancestry, Asian ancestry, or both has been observed in all West Eurasians sampled from the AMC."

While I like the clarity of the writing in this review (it is literally the fastest that I have read any paper), parts of the writing are overly cautious. Sometimes, they even enumerate literally *all* of the combinatorial possibilities of a situation as such:
"Specimens from the AMB that have been sequenced to date show that by this time modern humans in West and East Eurasia are similar to either Europeans or to Asians. There is also evidence of population structure in both ancient Europeans and Asians, as well as a notable mixture of European- and Asian-like ancestry in North Eurasia."

Still, a good read, especially for a lay-person like me :) thanks.

Aram said...

Rob

The y dna E could have emerged in Africa. Even E M35 could be present in Mesolithic NE Africa. But some subclades of E-M35 are very problematic to link to Africa. Mathieson in his recent revision qualified one of Levant Neolithic samples as a pre-E-M78. Genetiker simply called it M78.
I have serious doubts that we will see any M78 in Mesolithic Egypt older than Levant N. And keep in mind that this M78 is crucial for PAA.

Aram said...

Imho It is impossible to place E homeland in Horn of Africa. It is probably from North Africa.
Because we have numerous hunter's y dna from South of equator. And none of them is E !

Aram said...

What about Ust Ushim and Oase being from South Asia? Upper Paleolithic South Asia could be similar to them.

Anthro Survey said...

@Aram

Yeah, I definitely place things in a comfortable northeastern position, but wouldn't even be surprised if Egypt itself was an important early diversification zone(probably more so in Upper Egypt, if I had to guess). Btw, remember the pharaoh with E1b1a? Haplogroup noobs automatically assume ancestry south of the sixth cataract based on frequency, but no reason to think he wasn't your average local.

Also, the "tropical" traits associated with ancient Egyptians needn't at all be attributed to SSA. Think Papuans, Agta, Onge, etc. Just a preservation of some primordial traits suitable to that sort of environment on the part of their basal-most ancestry. I would imagine, of course, they decreased somewhat after a PPNB/C(?)-like influx(perhaps also packing more CHG) from the ME swept across NA.

We need to thoroughly scour Egypt for ancient DNA, imo. Nile, Fayyum, and all the oases in between.

Matt said...

@Rob, could have something to do with EHG, as EHG also show the same pattern of differences in relatedness to Han vs Tianyuan, but not due to ANE, as Fu seems pretty sure the patterns within the Villabruna group in relatedness to Native Americans vs East Asians are distinct.

@Davidski, thanks, both of those models *work*, with the model where X is shallowly on the Villabruna side of the tree and makes up most ancestry in Han working slightly better.

As a double check to see if anything is up with Han, would you mind running these?

Simple Bifurcation: https://pastebin.com/NjakMQRr (really to see how bad the worst stats are compared to the trifurcation model and check that it even is worse)
Trifurcation 1 w/Lapita Tonga: https://pastebin.com/xbUaXL7K
Trifurcation 2 w/Lapita Tonga: https://pastebin.com/gr2QSHRD

(If Lapita_Tonga isn't doable then Lapita_Vanutu, but if neither are doable, don't worry. This is just to check if adna produces different results than a modern East Asian group with higher heterozygosity, using the only ancient East Asian adna we have).

The worst stats for each of these Han-Villabruna-Tianyuan-Bichon graphs seem to be:

1 (X on the East side): Vil Han Tia Han, which I think should be equivalent to f3(Han;Tianyuan, Villabruna). Not sure how to interpret this.

2 (X on West side): Vil Han Vil Han, which is f2(Villabruna, Han).(f2 stats are basically such that f2(A,B) is equivalent to f4(A,B; A, B). See Ancient Admixture in Human History).

The f2 stat indicates the direct path in the phylogeny between A and B corresponds to the path on the phylogeny from A to B (the branch length between A and B). So this indicates that the path between Villabruna and Han is slightly too long here. Poss relates to El_Miron type ancestry but then that's getting the graph into more complex territory...

Davidski said...

@Matt

I don't have the Lapita genomes in my current datasets. I'll have to add them next time I update things.

Alberto said...

@epoch2013

I didn't quite follow your reasoning, so it's hard to answer. I think that admixture from WHG is quite easy to detect in other populations. We have it clearly there in El Miron, but not in any of the pre-25 kya samples.

All of the populations resurrecting from LGM went through a bottle-neck. But not in the Middle-East. So, if a migration from the Middle-East is the cause of WHG it had to be pre-LGM. But pre-LGM we don't see anything that matches.

25-22K YBP is indeed pre-LGM. We don't have one single sample between 25-20K YBP (unless I missed it).

@Matt

So at the moment we have: Villabruna and Bichon (almost simultaneous at 12,000 BCE / 11,700 BCE) and almost simultaneously Satsurblia cave sample and the Natufians.

If we're having a migration from east of the Balkans, then you need a simultaneous migration such that BEu was just arriving in both Satsurblia and Natufians (and so highly likely all the land between them) at exactly the same time the ME HG was leaving for Europe.

That seems like a lower probability event than that Villabruna is (largely) just Balkan Euro HG (since we have no Euro UP HG samples from the region) which shared ancestry with various HG in the Middle East at some point earlier in history (pre-BEu, or maybe one way if BEu was always there)


Though here I think we're a bit off with our timings. If El Miron (20K YBP) had some 30% WHG admixture (and assuming that WHG one way or another came from the east), that means that WHG entered Europe at 22K YBP. And none of the pre-25K YBP samples show this admixture. So I'm talking about 22-25K YBP.

The question is: Where was WHG 30K YBP? And where was BEu at that same time?

There could be a synchronization between the arrival of BEu to the Near East and the arrival of WHG to Europe, why not? One population pushing out another.

From the Balkans we have a sample from Romania and then one from Italy. It could be that Bulgaria or Greece had WHG already at 25-30K YBP, but where would they come from?

As I said, if we imagine a pure BEu population in the Near East since 70K to 15K YBP, we have a big problem explaining why this population didn't appear anywhere in Europe (including Eastern Europe, through the Caucasus). We'd have to argue that all Paleo Europeans came from Central Asia, and ultimately from South Asia in various waves, always avoiding those static Basal Eurasians.

Matt said...

@Alberto, if you assume that the Villabruna clade entered Europe 25-30kya and then hung out in SE Europe, until a later expansion, then yeah, I think those objections I raised on timing don't stand. Where they do stand is for a late UP entry of Villabruna clade directly from ME (rather than Villabruna clade->ME).

I don't think some degree of population isolation to allow for separate VB clade in SE Europe (which later influences ME) is particularly difficult in SE Europe - otherwise GoyetQ-116-1 ancestry isolation in SW Europe would be difficult. Obviously you have a lot of isolated demes in Eurasia at this point!

(No samples from Romania in Fu et al 2017 - what Upper Paleolithic EUR group pre-20kya sample are you referring to?).

Anonymous said...

Siberian Ust'-Ishim and European Oase1 had haplogroup K2a* (pre-NO). Tianyuan probably had haplogroup (pre-)NO. Here probably they had a small Denisovan admixture increasing to the East. Here, all of the Paleolithic Europeans got their admixture. However, the carriers of haplogroup R had no admixes Ust'-Ishim nor Denisovan admixes. Their direct unmixed descendants is EHG, while the ancestors of Villabruna (R1b, Epigravettian) and Loschbur (WHG) is the effects of mixing with Ust-Ishim (Western Siberia), Sunghirian (Eastern Europe) and Gravettian (Central Europe), which prevailed quantitatively.

D-stats
result: Mbuti.DG Ust_Ishim WHG EHG -0.010450192 -2.41164
result: Mbuti.DG Ust_Ishim MA1 EHG -0.020089471 -3.70820
result: Mbuti.DG Ust_Ishim AG2 EHG -0.008866979 -1.11543
result: Mbuti.DG Ust_Ishim MA1 AG2 -0.009094419 -0.91815
result: Mbuti.DG Ust_Ishim MA1 WHG -0.009781695 -1.88666
result: Mbuti.DG Ust_Ishim AG2 WHG 0.004410225 0.62273
result: Mbuti.DG Ust_Ishim Switzerland_HG EHG -0.014317936 -2.80288
result: Mbuti.DG Ust_Ishim Switzerland_HG WHG -0.003612584 -0.80423
result: Mbuti.DG Ust_Ishim Switzerland_HG AG2 -0.008332484 -0.96960
result: Mbuti.DG Ust_Ishim Switzerland_HG MA1 0.005289703 0.91316

result: Denisovan Mbuti.DG Switzerland_HG EHG 0.003869161 0.92158
result: Denisovan Mbuti.DG Switzerland_HG WHG 0.000877980 0.22465
result: Denisovan Mbuti.DG Switzerland_HG MA1 -0.008754743 -1.69163
result: Denisovan Mbuti.DG Switzerland_HG AG2 -0.000439171 -0.04369
result: Denisovan Mbuti.DG MA1 AG2 0.011549362 0.96735
result: Denisovan Mbuti.DG MA1 WHG 0.009605801 2.20976
result: Denisovan Mbuti.DG MA1 EHG 0.015858935 3.32853
result: Denisovan Mbuti.DG AG2 WHG 0.008303958 1.00786
result: Denisovan Mbuti.DG AG2 EHG 0.005761463 0.61286
result: Denisovan Mbuti.DG WHG EHG 0.003032299 0.90760
result: Denisovan Mbuti.DG EHG WHG -0.003032299 -0.90760

Anonymous said...

result: Denisovan Mbuti.DG Ust_Ishim MA1 0.002114132 0.42149
result: Denisovan Mbuti.DG Ust_Ishim AG2 0.006010413 0.68982
result: Denisovan Mbuti.DG Ust_Ishim WHG 0.010432135 2.38460
result: Denisovan Mbuti.DG Ust_Ishim EHG 0.014703908 3.23868

result: Denisovan Ust_Ishim Mbuti.DG Switzerland_HG 0.357929775 70.04208
result: Denisovan Ust_Ishim Mbuti.DG MA1 0.356524613 69.57029
result: Denisovan Ust_Ishim Mbuti.DG AG2 0.348008959 48.04443
result: Denisovan Ust_Ishim Mbuti.DG WHG 0.356066760 79.50094
result: Denisovan Ust_Ishim Mbuti.DG EHG 0.350162428 77.20417
result: Denisovan Ust_Ishim Switzerland_HG MA1 -0.001217722 -0.18318
result: Denisovan Ust_Ishim Switzerland_HG AG2 -0.008452737 -0.80553
result: Denisovan Ust_Ishim Switzerland_HG WHG -0.002899150 -0.56622
result: Denisovan Ust_Ishim Switzerland_HG EHG -0.011329119 -1.94882

Anonymous said...

@Alberto

The line of reasoning is this: We know WHG went through a bottleneck because we can see this in Loschbour and La Brana. We can also reasonably assume that was due to the LGM. We can reasonably assume the Mid.East didn't because we can see it in Hota IIRC. If there was admixture between an Middle-Eastern population and the LGM populations it would be visible in the Heterozygosity. I recall reading somewhere it isn't.

Anonymous said...

@Davidski

Iain Mathieson said the following on twitter w.r.t. the link between Anatolian and Iron Gates HG.

https://twitter.com/mathiesoniain/status/935883881777070080

"I mean the evidence is D(Mbuti, Anatolia_Neolithic, WHG, Iron_Gates_HG)=+7 but I don't know what the direction is."

Are the Iron Gates HG already available? If so, could you do D(Mbuti, Natufian, WHG, Iron_Gates_HG)?

Ariel said...

Weird map, I thought Karelia was near Finland and not near China

Grey said...

Alberto

"But again this is about probabilities rather than about what's just possible. Imagine that we know about this shared ancestry between West Asians and LUP/Mesolithic Europeans, so we'd have 2 competing hypotheses: Either a West Asian population moved to Europe or a European population moved to West Asia. And in principle (ignoring everything else), we could give each one 50/50 chances."

There's a 3rd logical possibility - that a population from a third region A moved to both region B and region C and then later (or simultaneously) disappeared from region A (or hasn't been found yet).

#

"You'd need that missing population not just to colonize all of Europe, but to venture deep into West Asia (including Arabian peninsula) and North Africa. That's quite an expansion for a hidden population from Europe."

Isn't there another possibility here also - say population A developed genes needed to survive in colder climates e.g. more efficient processing of iodine, and those genes provided a competitive edge further south or nearer a coastline where there was more base iodine in the food then maybe it didn't require a mass migration?

#

possible contenders for currently missing but significant populations might be 1) small nomadic steppe forager groups who despite having a very wide range left very little physical trace or maybe 2) wetlands foragers with by definition a very limited range geographically around lakes/seas and whose traces may be mostly under water.

e.g.

Matt

"The paper on Baikal Hunter Gatherers may be an interesting game changer here"

Matt said...

@epoch2013, interesting comment from Mathieson. I wonder why he would comment that "I guess that the Greek/Southern Balkan Mesolithic is mostly like Barcin but with more CHG and maybe more WHG, and there is gene flow with Iron Gates etc.". Why CHG? Not geographically simple...

Anonymous said...

Archaeogenomic analysis of the first steps of Neolithization in Anatolia and the Aegean, 2017

The Neolithic transition in west Eurasia occurred in two main steps: the gradual development of sedentism and plant cultivation in the Near East and the subsequent spread of Neolithic cultures into the Aegean and across Europe after 7000 cal BCE. Here, we use published ancient genomes to investigate gene flow events in west Eurasia during the Neolithic transition. We confirm that the Early Neolithic central Anatolians in the ninth millennium BCE were probably descendants of local hunter–gatherers, rather than immigrants from the Levant or Iran. We further study the emergence of post-7000 cal BCE north Aegean Neolithic communities. Although Aegean farmers have frequently been assumed to be colonists originating from either central Anatolia or from the Levant, our findings raise alternative possibilities: north Aegean Neolithic populations may have been the product of multiple westward migrations, including south Anatolian emigrants, or they may have been descendants of local Aegean Mesolithic groups who adopted farming. These scenarios are consistent with the diversity of material cultures among Aegean Neolithic communities and the inheritance of local forager know-how. The demographic and cultural dynamics behind the earliest spread of Neolithic culture in the Aegean could therefore be distinct from the subsequent Neolithization of mainland Europe.

http://rspb.royalsocietypublishing.org/content/284/1867/20172064

Alberto said...

@Matt

No samples from Romania in Fu et al 2017 - what Upper Paleolithic EUR group pre-20kya sample are you referring to?

From memory I recalled Romanian samples, and now a quick check reveals these ones:

Muierii2 - Romania - 33.700-32.800 cal BP
Ciclovina1 - Romania - 33.000-31.800 cal BP

Didn't take a closer look at the paper now to check what they say about them exactly, but I would remember if they were some kind of proto-WHG?

And 4 samples from Italy (assuming that with lower sea levels Italy was closer to the Balkans, though not sure if the Adriatic would still be a big barrier for them), between 34.000 to 27.000 cal. BP.

Matt said...

@Alberto - everything east of Italy is unassigned - http://www.molecularecologist.com/wp-content/uploads/2016/05/fuetal.jpg

So not proto-VB, but not part of the common Vestonice cluster. Adds weight that there is a population structure divide here, weakens idea that presence of Vestonice cluster in Italy, Vestonice, NW Europe precludes further structure in SE Europe (though not clear how much either of those actual samples could be ancestral to Villabruna!).

Shahanshah of Persia said...

@@Unknown You're an immature Indian nationalist masquerading as a Western European to lend credibility to your foolish claims. Yet, anyone with a brain cell can see through your ruse. Now be gone!

Mike the Jedi said...

Dave, I was reviewing the "Basal-rich" scores in your Basal K7 test. What percentage of that component do you reckon is actually Basal Eurasian? I think I remember you saying about half of it is, which would bring the Natufians down to ~37% BE. Have you any thoughts on this in light of this review or other more recent evidence?

Davidski said...

@Mike the Jedi

I haven't revisited the issue. But yes, probably about half of the Basal-rich component is Basal Eurasian, although this may vary for different populations, due to the way that ADMIXTURE works, so it's very difficult to be precise.

From memory, Matt looked at this issue in more detail than me, so he might be able to give you more insights.

Shahanshah of Persia said...

@Davidski Were Neolithic Iranians really 50% Basal?

Davidski said...

@Shahanshah of Persia

I don't know.

Matt said...

@Mike, I actually can't remember what conclusions we came to if any, might be worth looking at old threads.

I had an idea for estimating it prompted by your post: Use the component BRK7 Fst with Principal Coordinates Analysis to create a dimensional space representing the distance between components, then find a position which correlates to the Basal-Rich component level in populations, and is equidistant from the other Eurasian components, relative to distance from Africa. The defining characteristic of BEu is phylogenetic equidistance (relative to overall drift) from all other populations of Eurasia.

But I'm not so sure how worth doing this would be. If Fu's paper is talking about some admixture from a population X into Villabruna clade compared with UP Europeans, making Villabruna closer to Han without making it closer to Tianyuan, then I'd guess that makes it harder to distinguish with the dimensions in BRK7 between the Basal-rich component having more of that vs more actual Basal Eurasian... Still might be worth a try though, as a simple model.

Matt said...

@Mike, I've tried to do a few basic things on the Fst table for the components for Basal Rich K7 to work out how much BEu is in the Basal Rich component.

Put up a few screenshots on Imgur if you want to follow along.
First step, take the Fst table from BRK7, then use PCoA to transform into a set of dimensions for which the squared Euclidean distance captures the Fst matrix: https://imgur.com/oJt2SAp and https://imgur.com/ha5Y2cG

The dimensions that are output look like: https://imgur.com/89wXq1Q

Next step, I take the raw Fst distances from the original matrix and use them as variables; I use the Distance from Sub-Saharan as Variable 1, and I use the differences between relatedness to the other components (except Basal Rich itself) to construct a Variable 2, "Asymmetry" as a rough measure of relative relatedness between the other populations, where Asymmetry 0 indicates equal relatedness: (There are maybe some better ways I could've done Asymmetry, but the way I did seemed to work out OK): https://imgur.com/uB0Tifx

Then I produce a regression equation, which should let me estimate the position in these dimensions of a range of populations with different levels of drift that satisfy the Basal Eurasian criteria of equidistant relationship with other Eurasians: https://imgur.com/uB0Tifx

Then produce some simulated samples to go on it: (intuitively, they all fit on a line with Sub-Saharan, drifted away in the main dimension accounting for Eurasian vs African drift): https://imgur.com/ZDbgdrd

At the point, just doing manual tinkering, it seems like to get a population that has similar levels of overall drift to Villabruna and ANE and sits close to them in a phylogenetic tree, the best sim is for Basal-Rich to be about 20% Basal from between the lower drift Basal Eurasians and 80% hypothetical Middle East HG: https://imgur.com/oiGc570

Other solutions can be found to "make" Basal-rich from the simulated Basal populations, but these would all send the simulated "UHG" further away from Villabruna / ANE. If you have very high levels of BEu in Basal-rich, using these simulations, then the UHG has to have extremely high levels of drift away from other Eurasians and to be much more "West Eurasian" than VB or ANE is, in order to compensate. A low drift Basal population and a relatively typical West Eurasian population seems more intuitive.

Not sure if this method is all totally sound, but that's my best guess for Basal-rich component based purely on the component Fst and fitting using Fst PCoA - 20% Basal and 80% of UHG. That's extremely low compared to the lit though, I know. Poss some populations with extreme levels of BEu beyond Anatolia_Neolithic are not so well captured? Anatolia_Neolithic estimated with about 25% Basal Eurasian in Lazaridis 2016.

Mike the Jedi said...

@Dave
Thanks, Dave.

@Matt
Wow, you went above and beyond there, mate! Very much appreciate the effort. That analysis makes a lot of sense to me; I hope to see it confirmed or disconfirmed in the near future with the aDNA holy grail: a "pure" Basal Eurasian sample.

Our modern population references are robust, but there might be a few surprises left to uncover. Like the phenotypically interesting South Arabians:
http://anthromadness.blogspot.com/2016/05/mehris-are-fully-eurasian.html

I'd love to see their Basal and SSA levels.

Unknown said...


>http://eurogenes.blogspot.com/2017/07/working-topology-for-eurasian.html

In so far as that all Basal Eurasians were fairly closely related, and what really separates the Anatolian and the Iranian farmers is a lot of input from pWHG into the former

I don't think this topology is fully correct. There are clearly more differences between than just more WHG related admixture in Anatolia. Iran and CHG have much more ENA admixture (of few different types probably) which isn't shown here.

>Consider Kostenki14, GoyetQ116 and Oase1. They are highly different, even if K14 and GoyetQ116 are clearly from the same stock while Oase1 isn't. This might give an indication that ice age people were highly diverse.

Oase1/Ust'-Ishim seem to be Oceanian-like. Oase has elevated Neanderthal admixture which makes it seem more divergent than it actually is. Goyet/Kostenki/Vestonice/Sunghir aren't that different. Kostenki is probaly least differentiated out of the four, Goyet has Tianyuan related admixture and Vestonice is closest to Villlabruna Cluster. Sungir is inbetween Kostenki14 and Vestonice.

>Alberto, according to the recent Sikora paper, the dolni vestonice sample also has some WHG admixture, much earlier than El Miron
mtDNA U5 also appears in the Dolnis, U5 being the later archetypal lineage of the WHGs

So I think that suggests WHG might already have been arriving in Europe toward the middle UP; just prior the LGM- as a bridge from CE to SEE through to Anatolia, Caucasus etc

Vestonice probably had more of drift towards WHG than actual WHG admixture. I doubt WHG was fully formed at that time.

>And then we see a new population (WHG) colonizing Europe. From where? Not from Europe itself (since we have preceding samples from across the continent) and not from Siberia (we have samples too).

Probably from the Middle East. Middle Eastern UHG most likely had a distant common ancestor with it. Another option is that Vestonice-like populations evolved into WHG through drift but it's probably more complex than that.


>Poss some populations with extreme levels of BEu beyond Anatolia_Neolithic are not so well captured?

Neolithic Moroccans from Fregel seem to be very highly basal. Could you test them. It's also possible that "Basal Eurasians" where actually a very early mixed population. That would greatly complicate any admixture estimates.

Unknown said...


Like the phenotypically interesting South Arabians

Those Yemeni islanders look a bit like Sri Lankans. I wonder about their ASI levels.

https://imgur.com/a/RS1M2

Eren said...

@Matt:
I agree with Mike, very nice work mate! Always enjoy reading your comments and analyses.
Appropos, could you tell me how you did the regression of the Global10 samples to Davids new PCA?


@Mike:
That paper mentioned in the linked blog article got released with a different title, and the samples are freely available.
Link to paper: https://www.ncbi.nlm.nih.gov/pubmed/28913852
Link to dataset: http://datadryad.org/resource/doi:10.5061/dryad.1pm3r

Would be great if David could analyse them.

Matt said...

@Eren and Mike, cheers guys. In hindsight I think I may have overengineered it a little bit and the 20% number is probably a bit overprecise.

(I won't tl;dr but there are some questions about the higher dimensions capturing the Basal-rich component's specific drift, and how much of that should come from BEu or the HG side).

But I think the basics stand; 1) the Fst can be transformed to dimensions 2) Basal Eurasians should be neutral on all the dimensions that specifically separate other Eurasian components (apart from Basal-rich vs other) from each other, and that defines a line, 3) if we assume the other side has a roughly similar drift history (position) to what is shared by ANE, Villabruna-related, then...

To intersect all the right points, Basal-rich can't be more than 20-40% Basal Eurasian (anything more would mean that the HG side of Basal-rich would have to be drastically more heavily drifted than Villabruna component or ANE component, for one!) and Basal Eurasian has to have relatively low drift in the main dimension that separate Eurasians from African.

(Actually a high end number from that range like 40% would square the scores more easily with the results from lit for formal tests - something like 40% BEu in Basal-rich, then 55% Basal-rich in Anatolia_Neolithic, then you're close to the 25% that came in the Lazaridis 2016 formal testing.)

Matt said...

@Eren, to do the projection, steps were:

1) put both datasheets on the same spreadsheet

2) use a simple matching formula (countif) to match the IDs between the two sheets (Overlap was about 220 rows, including population averages. It would probably be higher if I'd used a Global10 sheet with modern day individual samples as rows rather than population averages only, and that might be marginally more of an accurate projection, as there could be a gain from having a bit more data to capture how dimensions between the two sheets covary).

3) remove rows which do not have a matching ID on both sheets, then sort them into the same order

4) merge both datasheets so you have one datasheet with 30 columns

5) copy the 30 column datasheet into PAST3.... (See - https://imgur.com/a/FG9Q9)

... and use the Linear>Model>Multi-variate function with 20 dependent variables (the ancient 67 world columsn), and the remaining 10 will be independent (Global10) variables. (See - https://imgur.com/a/Frrux)

6) take the output regression coefficients and then build a spreadsheet where the input Global10 variables can be processed through the regression equation.

This is the bit that's more complicated to explain, but the way I did this is to put all the regression data in a set of columns, then put the Global 10 data in the next columns, then another set of columns with formulas to run the regression. (So "=Ancient_67_PC1_Constant+(Global10PC1_to_Ancient_67_PC1_Coefficient*Global10PC1)+(M$5*$AK3)+(Global10PC2_to_Ancient_67_PC1_Coefficient*Global10PC2)+...."). If you know R, the efficient way (that I really should do) is probably not to bother with this just to write a script that does this (actually the whole process could be more efficiently done just as an R script!).

(Some screenshots here, if they actually help to make it any clearer: https://imgur.com/a/JV7Rc)

7) run the non-matching rows from Global10 through the regression/prediction spreadsheet, then merge back with the non-projected original data

Ryan said...

@David - "Which part? But I've swapped TreeMix for qpGraph, because there's generally much less fiddling around."

They seem to have: OOA -> EUR, Basal Eurasian, EAS

EUR+EAS->ANE

ANE into EUR

EUR+Basal->Satsurblia, Natufian

Or something along those lines.

Does that make sense? I'm talking about the 8 points listed in figure 1. Wonder if you can replicate them in qpGraph or whatever.

Unknown said...


>aDNA holy grail: a "pure" Basal Eurasian sample.

Morocco_IAM may be just that or nearly so.

Lenny Dykstra said...

I've wrote on anthrogenica before that was quite clearly an ANCIENT CENTRAL EURASIAN ghost population, which is responsible for the non-Basal portion of CHG and Iran_N's ancestry:

https://anthrogenica.com/showthread.php?11513-Pseudo-ANE-derived-from-Ancient-Central-Eurasian-ghost-population

The non-Basal ancestry in Natufians is something of a mystery, but I'd guess it was related in some way to some Mesolithic European HGs

Unknown said...

Also_there_are_two_Unknowns_in_this_thread.
Aryan_invasion_certainly_happened.

Eren said...

@Matt:
Thanks for the detailed explanation! I had gotten to step 5 myself earlier, but didn't really know what to do with that many coefficients. A bit complicated as you said, but your example definitely helped.

jparada said...

re: "pop X" in Han, i suspect such a thing doesn't exist. it's likely just minor steppe/west asian ancestry in Han raising their affinity to WHG.

Matt said...

@jparada, though that sort of structure (population shares reasonable amounts of drift with K14, GoyetQ-116,Vestonice16) should raise stats like D(Onge,Han;Vestonice16,Mbuti) / D(Onge,Han;Kostenki14,Mbuti), which if I recall correctly, is apparently not the case (basically 0).

Also not so clear how that explains why Han apparently would be more related to Bichon than Villabruna...

jparada said...

@Matt

i was under the impression that Han is marginally closer to Europeans than Onge is, please correct me if i'm wrong on this. On Bichon vs. Vilabruna, if i recall correctly, Bichon is closer to later West Eurasians than Vilabruna is, too.

Ryan said...

@Matt - The stats could still be 0 if there was both East Eurasian and Basal Eurasian admixture balancing each other, no? Which is essentially what Fu found?

Matt said...

@jparada, I can't remember seeing the stats, but if Villabruna clade and EHG generally are closer to Han than Onge, then it seems kind of hard that later Europeans wouldn't be, so sure. but the issue is why, if Han have any West Eurasian geneflow (rather than from an effectively trifurcated population), they would not any excess relatedness to UP Europeans...

I'm not sure if Bichon is closer to later West Eurasians than VB. You might have to look at the statistics in Lipson's latest paper for a hint. I don't think there's anything too consistent.

@ryan, which stats are we talking about? Any UP Euro descended pop plus with East Eurasian+BEu flow should theoretically look different in relatedness to Ust Ishim.

Unknown said...

>Also not so clear how that explains why Han apparently would be more related to Bichon than Villabruna...

Some calculators suggest that Bichon seems to have additional minor ENA admixtures(southeast asian, oceanian) which may explain him showing more affinity to Han than Villabruna.


Look at this:

Villabruna 14,180 ybp M236020
Eurogenes K15
# Population Percent
1 North_Sea 40.49
2 Baltic 28.24
3 Atlantic 22.57
4 Eastern_Euro 8.69
Using 4 populations approximation:
1 Lithuanian + Swedish + Swedish + Swedish @ 12.063459

M236020 (Villabruna Epigravettian) 14,180 ybp
Eurogenes ANE K7
Population
ANE 7.16
ASE 0.52
WHG-UHG 89.88
East_Eurasian 0.97
West_African 0.36
East_African 1.12
ENF –

Lochsbour F999918 8000 ybp
# Population Percent
1 North_Sea 34.51
2 Baltic 33.51
3 Atlantic 23.86
4 Eastern_Euro 7.33

Eurogenes ANE K7
Population
ANE 7.35
ASE 0.49
WHG-UHG 88.70
East_Eurasian 3.09
West_African -
East_African 0.36
ENF -

La Brana F999915 7000 ybp
# Population Percent
1 Atlantic 30.24
2 North_Sea 29.34
3 Baltic 28.15
4 Eastern_Euro 11.87

Eurogenes ANE K7
Population
ANE 3.98
ASE 0.45
WHG-UHG 92.37
East_Eurasian 2.31
West_African 0.86
East_African -
ENF -

Eurogenes K15

Bichon M600205 13,560 ybp
Admix Results (sorted):

# Population Percent
1 North_Sea 38.35
2 Baltic 26.09
3 Atlantic 24.86
4 Eastern_Euro 7.55
5 Southeast_Asian 1.22
6 Oceanian 1.1
7 Sub-Saharan 0.84

Single Population Sharing:

# Population (source) Distance
1 Swedish 11.38
2 North_Swedish 12.73
3 Norwegian 13.52
4 Southwest_Finnish 14.15
5 West_Norwegian 14.34
6 North_Dutch 14.35
7 North_German 14.59
8 Danish 14.94
9 Finnish 15.62
10 Irish 15.93
11 West_Scottish 16.29
12 La_Brana-1 17.03
13 East_German 17.27
14 Southeast_English 17.5
15 Orcadian 17.53
16 Estonian 17.59
17 Southwest_English 18.55
18 West_German 19.01
19 Hungarian 19.43
20 Polish 19.47

GoyetQ116-1 Kit M384220 30,000 ybp

Admix Results (sorted):

# Population Percent
1 North_Sea 19.91
2 South_Asian 16.98
3 Atlantic 16.96
4 West_Med 10.74
5 Baltic 8.92
6 Eastern_Euro 8.06
7 Oceanian 4.96
8 Southeast_Asian 4.85
9 Sub-Saharan 3.43
10 Amerindian 1.9
11 Siberian 1.19
12 Red_Sea 1.1
13 Northeast_African 0.99

Single Population Sharing:

# Population (source) Distance
1 East_German 21.65
2 South_Dutch 22.02
3 French 22.03
4 Hungarian 22.04
5 Austrian 22.08
6 West_German 22.51
7 Serbian 22.8
8 Spanish_Galicia 23.08
9 Moldavian 23.1
10 Croatian 23.37
11 North_German 23.8
12 Portuguese 23.89
13 Spanish_Cataluna 24.3
14 Southwest_English 24.4
15 Romanian 24.59
16 La_Brana-1 24.66
17 Southwest_Finnish 24.66
18 Spanish_Castilla_Y_Leon 24.76
19 North_Swedish 24.87
20 Southeast_English 24.89

Kit M236020 Villabruna 14,000 ybp

Admix Results (sorted):

# Population Percent
1 North_Sea 40.49
2 Baltic 28.24
3 Atlantic 22.57
4 Eastern_Euro 8.69
5 Oceanian 0.01

Single Population Sharing:

# Population (source) Distance
1 Swedish 12.56
2 North_Swedish 13.66
3 Norwegian 14.77
4 Southwest_Finnish 15.06
5 West_Norwegian 15.46
6 Finnish 15.94
7 North_Dutch 16.31
8 North_German 16.84
9 Danish 16.99
10 Estonian 17.1
11 Irish 18.31
12 West_Scottish 18.57
13 East_German 18.66
14 La_Brana-1 19.14
15 Orcadian 19.59
16 Polish 19.76
17 Southeast_English 19.8
18 South_Polish 20.07
19 Hungarian 20.39
20 Ukrainian_Lviv 20.46

Kit M225927 El Miron 19,000 ybp

Admix Results (sorted):

# Population Percent
1 North_Sea 28.2
2 Atlantic 28.1
3 Baltic 20.39
4 West_Med 7.05
5 Eastern_Euro 5.22
6 Southeast_Asian 4.23
7 Oceanian 3.17
8 Sub-Saharan 2.42
9 Amerindian 1.23

Single Population Sharing:

# Population (source) Distance
1 North_German 11.95
2 East_German 12.85
3 Irish 13.42
4 North_Dutch 13.56
5 South_Dutch 13.57
6 Danish 13.82
7 Southeast_English 13.87
8 Swedish 14.19
9 Southwest_English 14.2
10 La_Brana-1 14.23
11 West_Scottish 14.35
12 Southwest_Finnish 14.77
13 Austrian 15
14 Norwegian 15.07
15 North_Swedish 15.16
16 West_German 15.44
17 Hungarian 15.81
18 Orcadian 16.09
19 French 16.65
20 West_Norwegian 16.71

Anonymous said...

@Unknown

That El Miron run is interesting. The North Sea coast may harbour an extra tad Magdalenian.