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Monday, January 27, 2014

Poles more indigenous to Europe than Germans


This has actually been obvious for a while now, thanks to both modern and ancient DNA. But the figure below from the new Olalde et al. paper on the complete genome of a Mesolithic hunter-gatherer from Iberia illustrates it more effectively than anything else I've seen to date. Note that the Polish reference set (PL) shows significantly higher allele sharing with the ancient Iberian, La Brana 1, than do Germans (DE). In fact, only Swedes (SE) manage to better Poles in this regard. But it's also worth noting that Poles show the highest allele sharing with the two partial genomic sequences of Neolithic hunter-gatherers from Gotland, Ajv70 and Ajv52.


On the other hand, compared to Poles, Germans clearly show higher allele sharing with Gok4, the Neolithic farmer from Southern Sweden, and Otzi the Iceman from the Copper Age Tyrolean Alps. Unlike the hunter-gatherers, who are genetically more Northern European than any Europeans alive today, these ancient samples are more Mediterranean, and indeed more Near Eastern, than most present-day Europeans, which is something that can be seen clearly on the main Principal Component Analysis (PCA) from Olalde et al. below. This suggests that most of their ancestors arrived in Europe from the Near East during the Neolithic.


It's an intriguing outcome between these two large neighbouring European countries, but perhaps easily explained by geography and climate? Germany is situated west of Poland, so it has a warmer climate, and thus its territory was more heavily settled by early farmers from the Mediterranean Basin during the Neolithic. Moreover, much of what is now Germany was part of the Roman Empire, which might have facilitated gene flow between the ancestors of present-day Germans and southern Europeans.

Poles, on the other hand, show stronger genetic links to Baltic populations, especially Lithuanians and Estonians, who are arguably the most Mesolithic-like Europeans alive today (see here). In fact, if they were present on the graphs above, they'd probably easily top the allele-sharing list with La Brana 1 and all of the hunter-gatherers from Gotland. This might be due to the almost impenetrable primeval forests that once covered the areas just south and east of the Baltic, as well as the relatively cold climate in these regions.

Citation...

Olalde et al., Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European, Nature (2014), doi:10.1038/nature12960

See also...

The really old Europe is mostly in Eastern Europe

Prehistoric Scandinavians genetically most similar to modern Poles

Mesolithic genome from Spain reveals markers for blue eyes, dark skin and Y-haplogroup C6


52 comments:

S.K. Thompson said...

Might this be due to the fact that Poles themselves are more derivative of Baltic derived populations, while Germans as more Central European derived, tend to probably have a wider plethora of "European" variety.

I'd be curious though if one were to break Germans up between North-Germans(Danish/Scandinavian related), West-Germans(Dutch and Belgian related), East-Germans(Czechs), and South-Germans(Encompassing Switzerland, Austria, and France and differentiate individual-group realities from the aggregate of populations within Germany.

Germany, like France, Switzerland, and a variety of countries that fall within the sphere of "Central Europe" tend to be very genetically diverse, even to the point of having greater genetic distance within a said in-group versus an out-group ethnic group nearby.

Also, do you think that perhaps the greater EEF/ancient West-Mediterranean/East-Mediterranean components found throughout parts of Southern and to a lesser extent Western and Central Germany explain the tendencies found in your oracle for certain peoples from this area or with ancestry from this area to have certain Tuscan/Northern Italian/Fill in the blank Southern European tendency.

I've even seen Southern and West-Central Germans with strong East-Mediterranean tendencies drawing them back to Anatolia, the Caucasus region, and parts of far Southeastern Europe/Levant region, so I guess one is bound to have a lot of "normal surprises" when it comes to Germans.

Further, based on this logic, do you think that the indigenous of Poles might decrease the further they get pulled away from the core of the Baltic countries, especially Poles down closer to the Carpathian mountain region or parts of Central Europe near Slovakia.

Davidski said...

Yes, I've got a diverse set of Polish samples in my project now, from all over the country, and based on these I'd say the only Poles who might show elevated Mediterranean/Near Eastern admixture are those from the Carpathian foothills (where Balkan ancestry is evident) and also those with recent Jewish ancestry.

Also, I agree that if Germans were broken up into regional groups, then it's very likely that North Germans would equal Poles in terms of indigenous European ancestry. On the other hand, South Germans would be more similar to Hungarians and even groups from the Balkans in that respect.

And yes, the differences in Mediterranean/Near Eastern ancestry across Europe, dating all the way back to the Neolithic, will certainly be reflected in all of the tests in one way or another. In the latest Eurogenes test they'll show up as higher EEF, while in the other tests they'll result in inflated West Asian, East Mediterranean, West Mediterranean, Southwest Asian and Red Sea percentages.

About Time said...

The "East-Germans" (not just Czechs) were fairly diverse in origins, speaking a common language.

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

"1075/80, Adam of Bremen wrote about an emporium on an island in the Oder estuary, east of his Diocese, where Slaves, Barbarians and Greeks were supposed to live and Saxon merchants stayed for trade. Harald Bluetooth had once found refuge there."

http://en.wikipedia.org/wiki/Pomeranians_%28German_people%29

"In the High Middle Ages, Germans from what is today Northwestern Germany, Danes, Dutch and Flemish people migrated to Pomerania ... assimilating the West Slavic tribes of the Rani, Liutizians and Slavic Pomeranians."

In other words, these were open societies where pretty much everyone was mixing in these border towns (much like Norman England, I imagine).

Including the Slavic Kashubians, etc. http://en.wikipedia.org/wiki/Pomeranians_%28Slavic_tribe%29

The West German areas even more so, probably earlier assimilating socially mobile tradespeople from the Roman world during the dark age. Just like many skilled people left Rhineland etc and moved to U.S. in 1700's-1800's when opportunities in the new "border towns" (America) were better.

S.K. Thompson said...

I'm also curious, but could one consider Basques the archaic root of the Atlantic component, and if so could one say that Western Europeans, like British Islanders are some sort of combination of "Basque," and "Baltic," or is this too reductionist, as I'd expect it to be.

I already thing one could say that the Spanish are basically like archaic West-Mediterranean hunter-gatherer/farmer combined with Baltic hunter gather.

I'd expect the more Southern inclination of the populations like the Spanish and French to a lesser extent to be archaic bottlenecked "Middle-Eastern" of some more archaic root.

"Basque" populations seem to be more "Atlantic" in the archaic sense, because they themselves to be a "Western Mediterranean" population that assimilated "Baltic" archaic components(Might have something to do with La Brana and M'alta being related).

Its interesting to find though, although not surprisingly, that British Islander and even more Scandinavian derived populations tend to have more of this indigenous element, although not as much as Baltic and Finnic peoples.

I wonder though if British Islanders and Scandinavians are less indigenous because they absorbed more of the "Atlantic" component, which defacto makes them more bottlenecked "Middle-Eastern" in the archaic sense.

I bring this up because I'd be curious to wonder whether you think that the "North-Sea" component is really an "Atlanticized" Baltic component, and then defacto a kind of bottlenecked "Middle-Eastern" component by default relationship with West-Mediterranean(I know it gets fairly complex understanding diffusion in the context of ancient populations relating to modern ones).

If this is the case, and at least this is my thinking, but did "Baltic" and "North-Sea" separate during the Upper-Paleolithic or sometime even before this in the Finno-Ugric region or possibly somewhere in and around where "Eastern European" peaks out.

The next possibility I'd like to inquire about is whether it could be that "North Sea" and "Baltic" split during the Mesolithic era, as there was some genetic inflow beginning from West-Asia, the Levantine, and North-Africa into parts of Atlantic/Western Europe.

The last scenario seems that Neolithic diffusions split the "North Sea" component from "Baltic," and that the varying migrations during this time created the major changes that now really make a difference between "North-Sea" and "Baltic."

I'd just be curious if this falls in line with your reason, and I apologize for using such restrictive terminologies, but I found it the best way to remain simple and direct with my questions which include a lot of complexities.

Davidski said...

ADMIXTURE components at high K are usually a reflection of relatively recent demographic processes, like rapid expansions of linguistic or ethnic groups. So they're composites of the ancient ancestral components, often in very complex and cryptic ways.

For example, the best proxies for the Mesolithic people of the Atlantic fringe are actually Lithuanians. We know this from their extreme level of WHG. They're far from ideal, but certainly better than Basques, who have much more post-Mesolithic Near Eastern admixture. See here...

http://img835.imageshack.us/img835/7307/k36fig3.png

http://eurogenes.blogspot.com.au/2013/06/recent-gene-flow-from-africa-and-near.html

So the ADMIXTURE components that peak among the Basques are composites of both indigenous and foreign influences on the Atlantic fringe that are triggered by the long-term isolation and also rapid recent expansions of the Basques. These components then resonate among other groups that have the same or similar influences, like the western Irish.

Also, I doubt there was much genetic substructure among the Mesolithic hunter-gatherers of Europe, considering that it's the present-day people from the Baltic region that show the most affinity to Iberian hunter-gatherers, and the WHG and ANE components are very similar to each other.

The population densities during the Mesolithic all the way from Iberia to Central Siberia were very low, and the hunter-gatherers highly mobile, so there was probably constant gene flow across this vast area, preventing the formation of any strong substructures, especially within Northern Europe where there are no natural borders.

Mark Sakowski said...

Could this prove that there was a second migration of modern homo sapiens from Africa?

Davidski said...

Huh, what?

No, it proves that Germans have more ancestry than Poles from the Neolithic migrations into Europe about 8,000 years ago.

spagetiMeatball said...

David, is the EEF basically a stand-in for the total of neolithic ancestry? So for example sardinians are 80% neolithic near easterner, since they're 80% EEF?

Davidski said...

No, it seems that EEF is actually partly European, and not just Near Eastern farmer (ie. Basal Eurasian and Near Eastern WHG-like). So it's possibly around 25% WHG-like from the Balkans or even Central Europe. But Lazaridis et al. aren't sure how much exactly. This paragraph comes from page 61 of the supplement PDF.

"The amount of Near Eastern admixture estimated for Stuttgart can be seen in Table S10.2 and range between 61-98% with estimates increasing as the amount of estimated African admixture in BedouinB increases. Estimates using Dinka or Ju_hoan_North as an African outgroup are similar. There are reasons to doubt both the lower estimates (near 60%), since ALDER provides only a lower bound on African ancestry, but also the higher estimates (near 100%) since there is direct evidence that Stuttgart has European hunter-gatherer ancestry (Fig. 1B and Table S10.1). Determining the precise levels of Near Eastern admixture in Stuttgart must await further ancient DNA studies from both Europe and the Near East, but we can at least reasonably claim that most of the sample’s ancestry was Near Eastern, consistent with the mtDNA evidence for the Linearbandkeramik, which demonstrated a strong Near Eastern influence."

Fanty said...

"David, is the EEF basically a stand-in for the total of neolithic ancestry? So for example sardinians are 80% neolithic near easterner, since they're 80% EEF?"

No. I recall it was said, EEF is not the pure middle eastern input, but already a composit of the middle easterners with a "WHG-Like population".

In an earlier post, David thought this might be the WHGs of, for example the Balkan pensinsular.

If this is the case, the pure numbers suggest a higher middle eastern input than really was the case. It also would lower WHG numbers (as it doesnt count in those WHG that is bound inside EEF)

It would be the same problem as with modern "Components". Like modern components represent composits that had been created rather "recently", we now have 8000 year old composits. So EEF may represent European Neolithic farmer, but as a composit that started to exist on European soil and not the original middle eastern input.

barakobama said...


What is near eastern if the basal Eurasian thing is real? Doesn't this mean modern near easterns have a lot of basal Eurasian ancestry? So I don't think near eastern WHG-like is a good definition. Because near eastern may be a hybrid of WHG-like and basal Eurasian. Stuttgart was more related to Loschbour than any modern near eastern population is.

Does anyone know what Laz 2013 found about north Africans? In the admixtures they seem to be near eastern type, but I wonder if they are mainly from a third branch in the west Eurasian family.

barakobama said...

Fanty,

I think ANE may be mainly put into north European component(s) and that there is some EEF in them. Though I do think they are mainly Mesolithic European. I always knew Poles had more Mesolithic ancestry than Germans because they always score much higher in north European.

Even though EEF-WHG-ANE admixture has not been tested in every little region and ethnicity in Europe we can get I pretty good idea how they(especially EEF and WHG) are distributed by looking at other admixtures.

EEF seems to take in all forms of near eastern ancestry so it can't detect ancestry that may come from another near eastern people after the Neolithic or Neolithic ones that were far different from Stuttgart-Otzi-Gok4.

Most Europeans mainly descend from Loschbour type people and modern near eastern type people. Not Loschbour and Stuttgart type people. It is proven by F3 test or whatever the name is.

Quote from pg.7. It was the section that basically gave a summary of the paper. If you go down to table 1 you will see they didn't test all European and near eastern populations
"To test if present-day Europeans were formed by admixture of populations
related to Loschbour, Stuttgart and MA1, we analyzed f3(X; Ref1, Ref2) statistics which measure
the correlation in nucleotide frequency differences between a test sample and two populations:
(X-Ref1) and (X-Ref2). If the three populations are related by a simple tree, the statistic is
expected to be positive5. However, if X is admixed between populations related to Ref1 and Ref2,
the statistic can be negative and provides evidence of admixture in population X5. For each
present-day West Eurasian population, we tested all possible modern reference populations with
at least 4 individuals, along with Loschbour, Stuttgart, Motala12 and MA1 (Table 1). For the
majority of European populations (n=18) the lowest f3-statistic is observed with Loschbour and a
Near Eastern population as references, suggesting that many Europeans derive from a mixture
between WHG and populations related to present-day Near Easterners. Only Sardinians form
their lowest f3-statistic with Loschbour-Stuttgart so the mixture process is unlikely to have been a
simple WHG-EEF one (Table 1). Other European populations form their lowest f3-statistics with
MA1-Stuttgart, which we hypothesize reflects the cline of increasing relatedness to MA1 in Fig.
1B. In the Near East, no population has its lowest f3-statistic with Loschbour or Motala12, but all
have their lowest f3-statistic with Stuttgart (Table 1), suggesting that most of the ancestry of this
sample may be directly inherited from populations of the ancient Near East, while modern Near
Easterners have additional influences related to Africa, North Eurasia, or South Asia (Table 1)."

Davidski said...

If the Basal Eurasian component is real, then modern Near Easterners are mixtures of Basal Eurasians, ANE and Sub-Saharan Africans.

There's probably also room in that equation for something WHG-like but native to the Near East, and maybe ancestral to WHG? That's what I'm reading between the lines in the study, but maybe I'm wrong?

Davidski said...

"Most Europeans mainly descend from Loschbour type people and modern near eastern type people. Not Loschbour and Stuttgart type people. It is proven by F3 test or whatever the name is."

Most Europeans don't descend from modern Near Easterners, otherwise there'd be Sub-Saharan and even South Asian admixture all over Europe, but there isn't.

What the quote you posted is actually saying is that the same major admixture event affected almost all of Europe and the Near East after Stuttgart's ancestors migrated to Europe. The only part of Europe that wasn't affected for certain was Sardinia.

So obviously, they're talking about the post-Neolithic ANE expansion that moved from the east deep into Europe and the Near East, probably at about the same time. You can see that expansion on both the West Eurasian and global PCA that I posted on these blogs, because most Europeans and Near Easterners, and especially North/East Europeans and North Caucasians, are pulled east, even those that don't have any major Siberian admixture. BUT their clusters never overlap - they're perfectly parallel to each other. What this means is that whoever brought ANE into Europe didn't come from the Near East or even the North Caucasus, but rather from a source that was mostly ANE away from the Near East, like maybe the middle Volga region.

barakobama said...

Davidski, I don't mean most modern Europeans are mainly descended of combined modern between near eastern type and Loschbour type, or that ANE in Europe is from the near east.

What I meant is most modern Europeans fit better as admixed between modern near easterns and Loschbour than Stuttgart and Loschbour(Except for SARDINIANS). This means there is ancestry in modern near easterns that they share with most modern Europeans that Stuttgart(and modern Sardinians) did not have. I first suspected ANE being the reason.

It seems R1b originated in the near east that would mean the majority of west Europeans have a post-early Neolithic near eastern paternal lineage.

Also in admixtures I have noticed that non north European west Eurasian groups have different percentages across Europe. I definitely think there is post Neolithic near eastern ancestry in Italy(especially southern) and the Balkans(especially Greece). There is probably post Neolithic near eastern ancestry all over Europe except for in Sardinia(maybe a little).

There was ANE in Motola12 and it seems also in La Brana-1. So why couldn't there be ANE in the near eastern when Stuttgart's ancestors lived there? ANE in the near east definitely does not have an entirely Indo European source there is non Indo European ANE in Europe(Mesolithic and Uralic) and the near east.

Are the PCA's your talking about from "Another look at the Lazaridis et al. ancient genomes preprint ". The west Eurasian one is way to big to read even when I click on it and zoom in. On the one form Laz 2013 I don't see what you mean. I do understand what you described though.

Obviously ANE in the near east did not come from a heavily WHG people. Most may have come from an ~100% ANE people. For Europe I guess if what you say about the PCA is true that is evidence whoever brought ANE to many Europeans they did not have near eastern ancestry. By just looking at EEF-WHG-ANE percentages across Europe ANE coming to Europe from the near east seems unlikely.

The proto-Indo Iranians likely were heavy in WHG, EEF, and ANE and the Corded ware people(proto Balto Slavic) may have been very similar.

Davidski said...

"There was ANE in Motola12 and it seems also in La Brana-1. So why couldn't there be ANE in the near eastern when Stuttgart's ancestors lived there? ANE in the near east definitely does not have an entirely Indo European source there is non Indo European ANE in Europe(Mesolithic and Uralic) and the near east."

La Brana is same as Loschbour: WHG with 0% ANE. In other words, there was 0% ANE in Western Europe during the Mesolithic.

And we know there was 0% ANE in Western Europe and the Near East during the Neolithic because Stuttgart is 0% ANE.

Motala12 is SHG, with 19% of ANE. If we had Mesolithic samples from Eastern Europe, they'd have even more ANE.

So ANE expanded from somewhere around Eastern Europe/Siberia during the late Neolithic or Copper Age. Archeological and linguistic evidence fits better with an ANE expansion from Eastern Europe rather than Siberia, because it shows that the early Indo-Europeans probably came from the former.

But the ANE in the Near East, or even in parts of Europe, like in the south and southeast, need not be all of Indo-European origin. There were also expansions of non-Indo-Europeans like the Hurrians and the Kura-Araxes people, possibly from the Northeast Caucasus, just after the Neolithic. They might have carried mostly EEF, but also a lot of ANE, like Lezgins and Chechens do today.

barakobama said...

I feel guilty giving such a simple answer to where ANE in Europe and the near east comes from.

Stuttgart is prove ANE was absent in at least some early farmers in the near east. Uralic ANE could be explained because they like Indo Europeans came from the eastern edge of Europe. People like the Kura-axes and non eastern Mesolithic Europeans could explain some ANE. I think some ANE in the ear east could be pre Neolithic. I still don't understand, if nearly pure ANE people dominated far eastern Europe and central Asia for 1,000's and 1,000's of years where is their mtDNA?

I have heard that Olalde 2014 said La Brana-1 was more related to MA1 than any modern Europeans. Loschbour was much less related to MA1 than modern Europeans. So I assumed he had some ANE. La Brana-1 also looks part EEF in admixtures. Maybe the new date of around 8,000 years old is wrong.

Chechens and Lezgins in Eurogenes K13 converted to EEF-WHG-ANE are both about 13% WHG, 13% ANE, and 73% EEF. There is much more WHG in southern Europe from your Eurogenes K13 converted to EEF-WHG-ANE than in Laz 2013 but percentages are basically the same for the rest of Europe. Maybe high WHG and ANE Indo Europeans makes sense.

Fanty said...

"I think ANE may be mainly put into north European component(s) and that there is some EEF in them. Though I do think they are mainly Mesolithic European. I always knew Poles had more Mesolithic ancestry than Germans because they always score much higher in north European."

Well, "North European" was an artificial component based on modern Lithuanians. Simple as that.

They usualy scored 90% Northern European and 10% Ssouthern European or in some experiments even 100% NOrthern European...in this component.

After creating components with stone age men, modern Lithuanians apear to be...
46,4% WHG, 36,4% EEF and 17,2% ANE.

In other words... the "Northern European component" is a composit of these. Like.... 46,4%WHG+36,4%EEF+17,2%ANE = 90-100% "Northern European".

As we see, components created on modern people give us a distorted, sometimes totaly wrong picture.

Davidski said...

"I still don't understand, if nearly pure ANE people dominated far eastern Europe and central Asia for 1,000's and 1,000's of years where is their mtDNA?"

They obviously carried clades of mtDNA U, because many of the ancient samples from Eastern Europe and Siberia belong to U2, U4 and U5. Also, MA-1 was U*, remember?

But maybe mtDNA C is an ANE marker as well, because there's been some speculation at academic level that this haplogroup actually represents western-like admixture among modern East Eurasians.

That would certainly explain the mtDNA C among remains from Bronze Age Ukrainian Kurgans and the Tarim Basin (where there was loads of R1a too).

"Loschbour was much less related to MA1 than modern Europeans."

Where did you see this?

Loschbour and La Brana are both WHG, so if La Brana is closer to MA-1 than to modern Europeans, then so is Loschbour.

Of course, the reason La Brana is closer to MA-1 than to modern Europeans is because modern Europeans are largely EEF.

"Chechens and Lezgins in Eurogenes K13 converted to EEF-WHG-ANE are both about 13% WHG, 13% ANE, and 73% EEF."

I haven't looked at the calc results, but the study shows that Chechens and Lezgins have around 26-29% ANE.

Davidski said...

Fanty,

If you add up all of the hunter-gatherer-derived ancestry among Europeans, including the WHG-like admixture in the EEF, you'll get a decent enough correlation with this North European cluster, which peaks at around 77% among the Lithuanians.

http://bga101.blogspot.com.au/2012/04/so-whos-most-european-of-us-all.html

barakobama said...

What I heard was that la Brana-1 is most related to Baltic people(not a surprise at all), and MA1 is more related to La Brana-1 than to any modern Europeans(so I assumed La Brana-1 had some ANE). I never heard that he was more related to MA1 than to modern Europeans.

Can any of you give me one example from Laz 2013 were it says MA1 is very related to Loschbour. Besides being hunter gatherer populations in Eurasia that sometimes mixed I don't see how their connected. In all of the admixture graphs WHG and is shown as a broherclade to the non basal Eurasian ancestry in Stuttgart. Ancient north Eurasian is shown as a brotherclade to west Eurasian.

I made my own thread about Laz 2013. Maybe my opinion has changed a little bit since then.

http://www.theapricity.com/forum/showthread.php?111956-Lazaridis-2013-Ancient-genomes-suggest-three-ancestral-populations-for-present-day-Europeans

ANE to me seems related to west Eurasian and that's it.

MA-1 was apart of a mtDNA U(his own subclade) lineage that is now extinct. Loschbour had U5 yet no ANE admixture. I don't understand how the same mtDNA haplogroups could exist in two populations that had been separated for maybe over 50,000 years and before those haplogroups began.

U2e, U2d, U5(came as U* or pre-U5) and U4 may have come to Europe from different populations at different times who admixed to form WHG. RO members and very debated H members have been found in Upper Palaeolithic and Mesolithic Europe, not everyone was under U5, U4, or U2.

It seems the far eastern European hunter gatherers were entirely under U4, U2e, U5a, and some east Eurasian haplogroups. I know some might then say U5a is ANE and U5b WHG. But U5a existed all over Europe 10,000 years ago even in England(Chedder man was reported as U5a) and by where Loschbour lived(U5a has been found in Mesolithic Germany). U5 seems to be an exclusively WHG haplogroup. U2e, U2d, and U4 may have more complicated origins.

When I said north European I was talking about many different admixtures. Lithuanians I remember in globe13 scored something like 79% north European. Their WHG+ ANE=63.6%. Plus there is some WHG in EEF. Most people I remember agreed the north European components were mainly descended from Mesolithic Europeans like Loschbour.

If lets say 15% of EEF is actually WHG. Would that mean ~90% EEF in southern Italians adds 13.5% WHG and for ~30% EEF in Sami that adds 4.5% WHG? Do you get where I am going? EEF may be hiding the real percentages of WHG ancestry in Europe especially southern Europe. I doubt that though it is to simple and also Italy and the Balkans definitely have a lot of non Stuttgart near eastern ancestry which goes under EEF.

I can't wait till genomes are taken from Mesolithic or upper Palaeolithic east Europe for many reasons.

Aren't there suppose to be papers on the Gotland hunter gatherers, Funnel Beaker farmers, and St, Forvar(8,600 year old hunter gatherer from the Baltic sea) like there was on La Brana-1? Hopefully results from copper age Pontiac steppe will be out soon. They were early indo Europeans but just based on their dark eyes and light skin(based on near eastern mutations brought to Europe with farming) I bet they were high in EEF not WHG(maybe ANE). The samples are mainly from around the southwest coast of the black sea. The Rise project will tell a lot about the Corded ware people. Who I suspect to be very high in both WHG and ANE.

Fanty said...

Hmm.
Something just came to my mind...when I again thought about why on earth is there tons of farmer mtDNA in northern Europe but almost no Y-DNA.

Modern racial mix behavior...
I once read about a pattern in racial mixing.

It said. Black+White mixing today happens in the overwhelming most cases with a black male and a white female. White males, almost never mix with black females.

White - East Asian mixing is suposedly the other way around. Almost all white/yellow mix base on a white male with a yellow female.

I wonder if this would have been also influenced mixing between white EEF and black(brown) WHG? -.-

Davidski said...

"MA-1 was apart of a mtDNA U(his own subclade) lineage that is now extinct. Loschbour had U5 yet no ANE admixture. I don't understand how the same mtDNA haplogroups could exist in two populations that had been separated for maybe over 50,000 years and before those haplogroups began."

So what? Hunter-gatherers from Europe belonged to U*, U2, U4, U5 and U8. These are all different subclades of U.

http://img213.imageshack.us/img213/8204/futable1.png

Loschbour belonged to Y-DNA I, and La Brana to C6.

So why does MA-1, with Y-DNA R and mtDNA U*, who is more closely related autosomally to La Brana 1 than to modern Europeans and Asians, have to be something completely different?

Fanty said...

Found a new toy....
a website that analyses the attractivity of faces.

http://www.anaface.com/

I tested it with Brana and thats what it said:

He scores 7.15 of 10 (rather high in my opinion)

It said these are the reasons:

Bad because:

- poor symetry of face
- your ears are to big (well, I guess the size of those ears was imagination of the artist anyways?

- your face is too wide

- your nose is too wide for your face width

Good because:
- Eye distance ideal
- compared to nose width, mouth width is ideal (well wouldnt that mean mouth is too wide for face, if nose is too wide for face? ^^


Out of curiosoty I tested the farmer chick from Malta.
She scores 8.34 of 10

good:
good symetry

Bad:
Eye distance to wide (wtf?)
Nose too wide for that face width
Face too narrow anyways
The mouth is either to small for that nose or that nose to big for that mouth.

Funny... wonder if I should try that on myself? :-P

barakobama said...

Fanty, I was looking at the media's(exaggerated and partly untrue) articles about La Brana-1. I say some titled the first cute guy and it was from female centered websites. At CNN there was a girl or a few who said that la Bran-1 was hot. Maybe that face thing is accurate. Maybe they have done studies and know which facial features men or women are more attracted to. To me La Brana-1's reconstruction kind of looks like a Viking or what you would except a Mesolithic European to look like(paler skin though).

When you say "farmer chick from Malta" do you mean Stuttgart. I don't think there was a facial reconstruction of her. I am guessing she looked was a very stero typical Meditreaen type. Just look at modern Sardinians and you will get an idea what many farmers in Europe looked like during the Neolithic.

It would be interesting to see a reconstruction of Loschbour. His skull looks very archaic and definitely not Caucasian/west Eurasian(even though he was 100%). He had big eyebrow bones, big eye sockets, and a flat and wide nose. It is very different from la Brana-1's which looks very Caucasian.

La Brana-1 skull
http://www.google.com/url?sa=i&rct=j&q=&esrc=s&source=images&cd=&cad=rja&docid=7PdMwyLjuj056M&tbnid=_P9IsLrSSjFFrM:&ved=0CAUQjRw&url=http%3A%2F%2Fphys.org%2Fnews%2F2014-01-spanish-hunter-gatherer-blue-eyes-dark.html&ei=jFbtUvzSHcr9qAG6goCgDw&bvm=bv.60444564,d.aWc&psig=AFQjCNFiys_G1qqZsRT-kQ7biGrdHpauXA&ust=1391372298623599

Loschbour skull
http://www.google.com/url?sa=i&rct=j&q=&esrc=s&source=images&cd=&cad=rja&docid=sLWAqRU7mQO9JM&tbnid=zsLBWlL0-eylgM:&ved=0CAUQjRw&url=http%3A%2F%2Fforwhattheywereweare.blogspot.com%2F2013%2F12%2Fancient-european-dna-and-some-debatable.html&ei=11btUuudHIrnqAGhxIGoDw&bvm=bv.60444564,d.aWc&psig=AFQjCNFlpflJzOJ39EO3359SFm2zFXs3CQ&ust=1391372373322809

Loschbour was probably just a very unique and strange looking person. He could have been an outcast and is part of the reason he died young. I wonder why all these people died young. I would except that most ancient remains would be from people who died of old age.

Was it you had all those maps including a map of similar skull shapes to Mesolithic Europeans? It was very interesting and I hope it is legit. I wish I could find if my facial features are more hunter or farmer.


Fanty said...

"When you say "farmer chick from Malta" do you mean Stuttgart."

No. I mean the only reconstruction of a neolithic female skull all over the net.

A woman from the mediteranean island "MALTA".

I putted her face on one of the picture collections I did.

Here is another reconstruction of quiet typical phenotypes of pre-neolithic Europe. (and someone placed Tennisplayer Andre Aggasi next to him, because he really looks like that reconstruction. X-D

http://mathildasanthropologyblog.files.wordpress.com/2008/08/seperated-at-birth.jpg

But its outdated... it has brown eyes... (Because at that time, when the reconstruction was done, they thought blue eyes did not exist at that time) and we know those people seemed to have blue ones.

"I wish I could find if my facial features are more hunter or farmer."

Is there any celebrity that looks like you? ^^

barakobama said...

Fanty, you should grow a full beard black-blonde-red your lucky. Some people have multiple hair colors but mainly one for head hair, one for facial hair, and one for body hair. Not all put together into one section.

I have all three but in different sections. I could give you many examples from my extended family of blonde hair that turned dark, red facial hair but blonde head hair, brown skin but red chin hairs, etc.

There are many shades in-between dark-blonde, dark-red, and blonde-red. There are many people with light or dark head hair but red facial hair. In pre-school most kids have bright blonde hair but by 8th grade most have very dark hair.

It is also difficult to define eye color at times. Some people define intermediate colors as blue. It seems based on the 8-plex eye color predictor intermediate colors are in-between brown and blue.

I think pigmentation is so complex that there may be no perfect way to tell what someone has by looking at SNP's.

Fanty said...

Thats the eyecolor that gedmatch predicts for me:

http://ww2.gedmatch.com:8006/autosomal/bceb31_11_.jpg

based on:

CC at: rs3794604 - Blocks some melanin. Often gives light colored eyes.
GG at: rs7174027 - Blocks some melanin. Often gives light colored eyes.
CC at: rs4778241 - Low Melanin. Basis for Gray, Blue, Green, or Yellow Eyes if no other pigmentation is present.
CC at: rs9782955 - Blocks some melanin. Often gives light colored eyes.
CT at: rs989869 - Contrasting sphincter around pupil.
CT at: rs3947367 - Contrasting sphincter around pupil.
AA at: rs8033448 - Med Brown on Sphincter
AA at: rs1105879 - Weak Amber Gradient
AA at: rs4778138 - Weak Amber Gradient
GT at: rs1470608 - Medium melanin on Anterior Epithelium. Gives dark eyes.
GG at: rs7277820 - Penetrance modifier, Blue.
GG at: rs16891982 - Starburst (Collarette)
TT at: rs1667394 - Starburst (Collarette)
CC at: rs12203592 - No pigmented Collarette.

barakobama said...

I have seen that pre Neolithic European reconstruction before. It is likely that man had blue or brown eyes. Not every Mesolithic European had blue eyes. Remember everyone used to have brown eyes and we don't know when brown mutated to blue. I can't tell the difference between different west Eurasian people in facial features. All I can say is the reconstruction of that man looks Caucasian.

Here are some reconstructions of I saw at a Lascaux exhibit.

http://mathildasanthropologyblog.files.wordpress.com/2008/08/seperated-at-birth.jpg


http://www.google.com/url?sa=i&rct=j&q=&esrc=s&source=images&cd=&cad=rja&docid=PE8juyYlwmj6uM&tbnid=f7z2PPNRcWoKuM:&ved=0CAUQjRw&url=http%3A%2F%2Ffrenchculture.org%2Fvisual-and-performing-arts%2Fevents%2Ffabulous-lascaux-caves-houston&ei=vnPtUpSeI83YyAGt64D4BA&bvm=bv.60444564,d.aWc&psig=AFQjCNHf74jcJX0rs80Es13SWu9rBzJx0A&ust=1391379186925892

http://www.google.com/url?sa=i&rct=j&q=&esrc=s&source=images&cd=&cad=rja&docid=uBpxqX4eWzztkM&tbnid=hkUOv_ZrIDNfoM:&ved=0CAUQjRw&url=http%3A%2F%2Fforum.nationstates.net%2Fviewtopic.php%3Ff%3D31%26t%3D281050%26start%3D50&ei=1nPtUp67B6PsyQH7nYHwBg&bvm=bv.60444564,d.aWc&psig=AFQjCNHf74jcJX0rs80Es13SWu9rBzJx0A&ust=1391379186925892

http://www.google.com/url?sa=i&rct=j&q=&esrc=s&source=images&cd=&cad=rja&docid=ktcJUN2kPql5iM&tbnid=bJ-Ow1-m3f9hBM:&ved=0CAUQjRw&url=http%3A%2F%2Fchicagotonight.wttw.com%2F2013%2F03%2F21%2Fstone-age-chicago&ei=7XPtUrjfCaqoyAHuzoGICg&bvm=bv.60444564,d.aWc&psig=AFQjCNHf74jcJX0rs80Es13SWu9rBzJx0A&ust=1391379186925892

http://www.google.com/url?sa=i&rct=j&q=&esrc=s&source=images&cd=&cad=rja&docid=ktcJUN2kPql5iM&tbnid=bJ-Ow1-m3f9hBM:&ved=0CAUQjRw&url=http%3A%2F%2Fchicagotonight.wttw.com%2F2013%2F03%2F21%2Fstone-age-chicago&ei=7XPtUrjfCaqoyAHuzoGICg&bvm=bv.60444564,d.aWc&psig=AFQjCNHf74jcJX0rs80Es13SWu9rBzJx0A&ust=1391379186925892

This figurine is supposable 28,000 years old. It is from the Dolni Vestoncie site in Czech Republic.
http://www.google.com/url?sa=i&rct=j&q=&esrc=s&source=images&cd=&cad=rja&docid=QC79k7M0RjlJsM&tbnid=10I79qot_9C4SM:&ved=0CAUQjRw&url=http%3A%2F%2Fdonsmaps.com%2Fhoax.html&ei=A3ftUo3NGcKsyAG51YCYCw&psig=AFQjCNEjQqQeuORLMmgWPi0VycHEmu8Qbg&ust=1391380184407924

Here are some carvings of human faces in La Mrache cave(west France) dated as ~15,000 years old. Below is a link about la Marche from Wikipedia. The carvings may be fakes.

https://www.google.com/search?q=Lascaux+exhibit&source=lnms&tbm=isch&sa=X&ei=cXHtUofcEemQyAH6lYG4Bw&ved=0CAcQ_AUoAQ&biw=1024&bih=651#q=la+marche+cave+carvings&tbm=isch&imgdii=_

barakobama said...

http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=2&cad=rja&ved=0CDQQFjAB&url=http%3A%2F%2Fen.wikipedia.org%2Fwiki%2FLa_Marche_(cave)&ei=WnjtUsrlJc64yAGWroG4Bw&usg=AFQjCNF1qdmbV5bjcBBxhbOIKMq265GVlA&sig2=_ZW63jB-68h4P9pQm3jhlw&bvm=bv.60444564,d.aWM

barakobama said...

"So what? Hunter-gatherers from Europe belonged to U*, U2, U4, U5 and U8. These are all different subclades of U.

http://img213.imageshack.us/img213/8204/futable1.png

Loschbour belonged to Y-DNA I, and La Brana to C6.

So why does MA-1, with Y-DNA R and mtDNA U*, who is more closely related autosomally to La Brana 1 than to modern Europeans and Asians, have to be something completely different?"

I never remember laz 2013 stating MA1 is more related to Loschbour than to any modern Europeans and Asians. In all those trees ancient north Eurasian was put as a brother clade to west Eurasian. MA1 is just as closely related to eastern non Africans as Loschbour and the Motalas are, and according to Raghavan 2013 there is evidence he was basal west Eurasian Autosomally. That's all i know about MA1 he seems to be very related to west Eurasians.

Either La Brana-1 has a lot of ANE or WHE and ANE are closely related. Y DNA C1a2-V20 in Mesolithic Europe makes more sense than Y DNA R. The reason is every descendant of Y DNA K-M256 is very exclusive to eastern non Africans except P(including P*, R, and Q). Y DNA C is so basal that it makes sense a branch exists in Mesolithic Europe like it makes sense F-96 or I did.

Still U5, U4, U2e, and U2d seem to have developed in WHG and ANE. How do they have the same maternal lines if many didn't mix? I consider what you say but i still don't get how it is possible ANE also had a lot of U5, U4, and U2.

Fanty said...

Barak, have you seen this one?

http://img9.imageshack.us/img9/7450/oz6i.png

It says, if the alleles of EED, WHG and ANE are compared, the least comparable pairing is EEF and WHG.

And it says that in those contrasting alleles, ANE is more "WHG like" than its "EEF like" if it would be something totaly different it would remain in the neutral position (0) but it pulls towards WHG.

The second axis tells us the difference between WHG and ANE. (thats why they apear so far apart. Its not about the shared alleles of both but about not-shared ones. And EEF pulls towards WHG, most likely because of its early WHG admix.

And that image here:

http://img20.imageshack.us/img20/9159/6g9k.png

Suggests that alleles that WHG and EEF do not share, are responsable for the difference between North and South Europe. And that the alleles that make the difference between WHG and ANE ( one could say, the "exclusive ANE" alleles. Whatever that may be (Amerindian like alleles? Whatever?), are the ones than make the difference between West and East Europe.

That should be the tendency at least.

barakobama said...

Thanks for those links Fanty. It is exactly what I have been looking for, EEF(Stuttgart), WHG(Loschbour), and ANE(MA-1) comparison. Is it from Laz 2013 and Stuttgart represent EEF, Loschbour WHG, and MA-1 ANE right?

From top to bottom EEF is closest to WHG from left to right ANE is closest to WHG.

Obviously ANE is more related to WHG than it is to EEF. There was no east Eurasian admixture in MA-1 so he was pure non east Eurasian and probably some form of west Eurasian or closely related. I still think it is possible MA-1 was a mutt. What is his relation with south Asians? MA-1 could have been mixed between many related west Eurasian peoples(including Upper Palaeolithic European proto-WHG) who distributed ancestry that we put all under ANE.

It is pretty interesting that WHG seems to be closer to ANE than to EEF. Could basal Eurasian be the reason? Maybe there was a population very related to WHG in the near east but basal Eurasian makes EEF less related.

No one knows exactly how WHG was formed. Is it a mixture of something from upper Palaeolithic near east and something very related to ANE? There are many different possibilities. I still think the reason MA-1 is more related to La Brana-1 than any modern Europeans and Asians(native Americans?) is evidence WHG and ANE are very related or that La Brana-1 had a lot of ANE.

Europeans are pulled to the right by WHG and ANE, pulled to the left by EEF, pulled down by ANE, and pulled up by EEF and WHG. It is pretty constant with WHG, EEF, and ANE admixture percentages. There may be other factors though that cause the position for many Europeans.


"Suggests that alleles that WHG and EEF do not share, are responsable for the difference between North and South Europe. And that the alleles that make the difference between WHG and ANE ( one could say, the "exclusive ANE" alleles. Whatever that may be (Amerindian like alleles? Whatever?), are the ones than make the difference between West and East Europe.

That should be the tendency at least."

Totally agree. Except some southern Europeans(and Ask Jews) are as pulled far down towards ANE as east Europeans are or even more. Also north-east Europeans are pulled more to the right towards WHG than anyone. ANE difference is not the only difference between east and west Europeans.












Fanty said...

"Totally agree. Except some southern Europeans(and Ask Jews) are as pulled far down towards ANE as east Europeans are or even more. Also north-east Europeans are pulled more to the right towards WHG than anyone. ANE difference is not the only difference between east and west Europeans."

Another strange thing in this image is:

If Scottland and Ireland really have much more ANE than England and ANE is responsable for west/east contrast, why doesnt it make them more east than English on PCA or MDS.

Fanty said...

Hmm. When Georgians had been responable for the East-Pole it was more clear.

Georgians share lots of Alleles with the north of the middle east AND they share a lot of alleles with ANE too.

So they work as a magnet for ANE anchestry (affects northern and eastern Euros and middle east like anchestry (pulls things like southern Italy to the east) both.

barakobama said...

I already posted in this thread that Caucasian populations Chechens and Lezgins both scored about 13% WHG, 13% ANE, and 73% EEF. Their Eurogenes K13 results were converted to EEF-WHG-ANE. I would not be surprised if Georgians would score some WHG. I am not sure if it is WHG or a very related form in the near east.

Does it really matter what populations you put in that PCA with EEF, WHG, and ANE? If you put in south Italians instead of Finnish that will affect where other populations are placed?

If MA-1 is so related to Mesolithic Europeans then why didn't Laz 2013 say so. Wouldn't they have suspected MA-1 related ancestry in Loschbour? Couldn't ANE and WHG be confused with each other? It doesn't seem that happened though. It really complicates things to say ANE and WHG were like brothers.

It is interesting though because I have heard Mal'ta site had the same type of venus figurines that have been found all over upper Palaeolithic Europe. 31,155 year old Pre-U5 was found in the Dolni Vestonice site which had some venus figurines. So directly connected to later U5 dominated WHG.

Would ANE and WHG have split in the Upper Palaeolithic? How likely is it that Y DNA R(very related to east Eurasian lineages) originated in WHG-ANE people? An origin in south Asia for Y DNA P and R makes the most sense to me.

Davidski said...

"If MA-1 is so related to Mesolithic Europeans then why didn't Laz 2013 say so. Wouldn't they have suspected MA-1 related ancestry in Loschbour? Couldn't ANE and WHG be confused with each other? It doesn't seem that happened though. It really complicates things to say ANE and WHG were like brothers."

They did say so. They even gave a couple of equations. Start at the bottom of page 92 in the supplement info PDF. What this part discusses is how some North Caucasians carry more ANE than Europeans, and yet Europeans are much closer genetically to MA-1 than North Caucasians are. The reason for this is that Europeans are largely WHG.

"However, the high MA1-related admixture in Northeast Caucasians seemingly contradicts Extended Data Fig. 4 which shows many Europeans to have even higher values of the statistic.

This is not in fact a contradiction, however, because for Europeans the statistic can be written as...

The first term vanishes, and both other terms are positive, since B and MA1 are sister clades and Loschbour and MA1 share drift that Stuttgart lacks because of its basal Eurasian admixture, with f4(Loschbour, Stuttgart; MA1, Mbuti) = 0.004573 (Z= 6.799)."

Fanty said...

"Does it really matter what populations you put in that PCA with EEF, WHG, and ANE? If you put in south Italians instead of Finnish that will affect where other populations are placed?"

It absolutely matters what you put into a PCA/MDS.

If you put different populations, you get a picture that looks similiar, but the proportions can be totaly different.

The populations in the extreme positions are the ones that matter.

In the typical Euro MDS, the software picks up Sardinian versus Finnish as the greatst difference and puts anyone else into that contrast. If you take them away it will take Lithuania-Southern Italy and the axis will look similiar but not identical.

The second dimension is less informative because it doesnt contain all informations.

Typical 2. Dimension would be Basque versus Georgians but the alleles that define Sardinia versus Finland are out of the game.

In the third dimension you get a wedge with wedges running from Norway over Poland, Russia, Baltic states to Finland and from Norway over the other Germanic speaking countries over western Europe, southern Europe to Greece. But it doesnt use the alleles already used for dimension 1 and 2. It ends that dimension 4-6 become more and more diffuse or seem uninformative because they base on less and less alleles.

If you use only a few countries like say..... Britain-Netherland-Germany-Hungary then the only dimension that seems to make any sense is the first. The second dimension may pick up the contrast between two English...

Matt said...

Davidski: Of course, the reason La Brana is closer to MA-1 than to modern Europeans is because modern Europeans are largely EEF.

No offence, I think this is kind of wrong.

If you look at figure 5e from Olalde, where there is a clear La Brana drift sharing axis, it's clear Mal'ta is only closer to La Brana than 1 out of 8 European samples (and tied with another European sample).

http://www.nature.com/nature/journal/vaop/ncurrent/fig_tab/nature12960_SF5.html

Btw, generally, with your interpretations of Laz's models here, I get the impression you may be slightly overestimating the closeness of their modeled WHG and ANE here while slightly overestimating the dissimilarity of their modeled basal Eurasian from both.

If you look at the distance stats from Laz, for instance in the French fit of their model (fig Figure S12.11), the West Eurasian and Ancient North Eurasian group are separated by a distance of 80. Both of them are also separated from Basal Eurasian by about 117-119, or let's call it 120.

So the distance from ANE-WHG is about 66% that of the distance of either from basal Eurasian.

As such, it's clear that a population which was mixed 50% basal Eurasian and 50% WHG (as EEF is more or less estimated to be) would be closer to WHG than ANE is. Because its drift from WHG would be only 50% of basal Eurasian's from WHG, while ANE's drift is 66% of basal Eurasian's drift from WHG.

Small differences in drift in descendants would change the calculus of relatedness slightly though.

This might shed some light on why modern Europeans are closer to La Brana than Mal'ta appears to be, as per the above graphic from Olalde.

Davidski said...

Matt,

WHG and ANE are separated by 16,000 years, so it's not surprising there's a lot of drift between them. They're still sister clades though (or at least ANE is a sister clade with the ancestor of WHG), and they affect significantly each others' affinity to present-day samples (for instance, modern Europeans are more ANE-like than Northeast Caucasians because of WHG admixture, even though Northeast Caucasians have more ANE admixture) . This is what Barak is missing.

The other issue, however, is what happened in those 16,000 years. Afontova Gora 2 is much closer to modern Europeans than MA-1 is, while Motala12 is 19% ANE, whatever that actually means. So were ANE and the ancestors of WHG actually separate populations in those 16,000 years? It doesn't seem so to me. What I'm still convinced of is that in WHG and ANE we're looking at the western and eastern extremes of the same Northwest Eurasian forager gene pool, but the difference between them is being exaggerated by inadequate sampling across time.

barakobama said...

Davidski it is interesting how close ANE and WHG are in that PCA, that MA1 is closer to La Brana-1 than to any modern Europeans or Asians, and that Europeans are more related to MA-1 than Caucasians even though they have so much ANE admixture.

Laz 2013 seems to think Basal Eurasian ancestry is the reason Europeans are more related to MA1 and that Loschbour and MA1 share "drift" Stuttgart does not.


"However, the high MA1-related admixture in Northeast Caucasians seemingly contradicts Extended
Data Fig. 4 which shows many Europeans to have even higher values of the statistic.
This is not in fact a contradiction, however, because for Europeans the statistic can be written as.....

The first term vanishes, and both other terms are positive, since B and MA1 are sister clades and
Loschbour and MA1 share drift that Stuttgart lacks because of its basal Eurasian admixture, with
f4(Loschbour, Stuttgart; MA1, Mbuti) = 0.004573 (Z= 6.799).

By contrast for North Caucasians....

Intuitively, the shared drift shared between a test population and MA1 is diluted by Near Eastern
ancestry (because of the Basal Eurasian ancestry in the Near East), and augmented by WHG ancestry (because of the lack of Basal Eurasian ancestry in Loschbour)."

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

They also say Basal Eurasian ancestry is why east Eurasians are more related to MA1, Loschbour, and Motala12 than to Stuttgart.

I don't know how those graphs work but near east and WHG are always shown as brothers. EEF is suppose to be a mixture of near eastern, Basal Eurasian, and WHG right? Basal Eurasian explanation given by Laz 2013 may be true. Maybe the west Eurasian form of near eastern is more related to WHG than ANE is.

I agree EEF(or more ANE in La Brana-1) is the reason MA1 is more related to La Brana-1 than any modern Europeans(and Asians). Then question needed to be answered is what in EEF causes this. It could be Basal Eurasian and west Eurasian form of near eastern could still be more related to WHG than ANE is.

It does seem likely to me that WHG and MA1 are more related to each other than to whatever form(s) of west Eurasian there is(are) in the near east(everyone forgot about north Africa).

Basal Eurasian can help answer the questions but I think WHG and MA1 being closely related is the main reason. I had already suspected WHG were descended of Europeans from over 20,000 years ago. It could not have just been west WHG and east ANE though. There would have been intermediates and mixing between groups all over north Eurasia. This stuff is so complicated I am going to have to start writing down all my thoughts.

I guess it would be called ancient north Eurasian. Because Europe is set up north like Siberia. I think it is likely all the land from Portugal to eastern Siberia was mainly inhabited by these people during the Upper Palaeolithic. It makes sense Venus figurines like the ones in Europe were found in the Mal'ta site. It seems these Upper Palaeolithic north Eurasians are who used to be called Cro Magnon.







Davidski said...

Have you heard of the Natufians? They used to live in the Levant. Maybe they were the Basal Eurasians?

http://mathildasanthropologyblog.wordpress.com/2008/03/09/the-natufians/

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

Matt said...

Davidski - The other issue, however, is what happened in those 16,000 years. Afontova Gora 2 is much closer to modern Europeans than MA-1 is, while Motala12 is 19% ANE, whatever that actually means. So were ANE and the ancestors of WHG actually separate populations in those 16,000 years? It doesn't seem so to me. What I'm still convinced of is that in WHG and ANE we're looking at the western and eastern extremes of the same Northwest Eurasian forager gene pool, but the difference between them is being exaggerated by inadequate sampling across time.

Interesting, and this is probably an extreme awkward question, but is AG-2 closer across a European and MA-1 ascertained axis or just generally closer?

I could imagine a process where the extremes of the range continuously experience population contact and drift with one another, so they may not be closer to one another than their ancestors, but if you checked their drift against an axis ascertained against their ancestors, they'd be closer on that.

That would fit with the extremes of a range idea.

I think that's kind of what we see with Laz's models of Motala - it seems to have some admixture ANE, aka from the eastern extreme of the range northern range, plus some new drift of its own (although it seems like it is hard to say how much at the moment due to sequence quality).

Especially if this was also happening at the other end of the range, the ends might not get any closer to one another over time, despite being admixed of the ancestors from each end of the range. (They'd also be relatively closer compared to their drift from a unrelated, non-mixing population)

If that's the case though, it's also true that Mal'ta would seem more central across a present-day West Eurasian ascertained axis than it is, while AG-2 should be more spread out.

More ancient genomes from the northern belt, as you say, will be really help clear this up a lot.

Davidski said...

It looks like there's a cline running from the Americans to Europe, and AG-2 is closer along that cline to Europe than MA-1 is. That's the case on both the plots, even though the Amerindian samples are projected onto the West Eurasian plot.

http://img853.imageshack.us/img853/684/u26w.png

http://img203.imageshack.us/img203/2267/g0zb.png

If the ancestors of ANE split from the ancestors of WHG well over 24,000 years ago (because MA-1 is that old), followed by at least 16,000 years of separation (because Loschbour is 8,000 years old), then shouldn't AG-2 be further away from Europe than MA-1 is, due to many thousands of years of extra drift away from the WHG gene pool?

It seems they never really split. Rather, it appears that at the very least they had intermittent but significant contacts with each other across the taiga belt. So where do we draw the line between WHG and ANE, especially if we're lacking those 16,000 years in genetic drift between the individuals that are being compared?

Or maybe I'm just not getting something because I can't comprehend the intricacies of both space and time here? I guess we'll see.

About Time said...

The spaces here are hard to fathom. AG2 is way north, north of Baikal. That people were in contact at all between these (still) remote areas gives pause to consider the tenacity of early humans in these punishing environments. Not only that, but moving around places like that (and surviving) means people had knowledge of geography and passable travel routes from very very old times.

And moderns balk at the notion of Iron Age movements within the warm and easy temperate zones?

barakobama said...

Was MA-1 west Eurasian or something else? I am still very confused.

In PCA's MA-1 is always in-between Europeans and south-central Asians and somewhat close to native Americans.

Olalde 2014 says MA-1 is more related to MA-1 than he is to any modern Europeans or Asians(do they mean east Asians?). Laz 2013 and Raghavan 2013 say MA-1 had no relation to modern east Asians. Laz 2013 found he had no more relation to east Asians than Loschbour and Motola12 did. Raghavan 2013 says there is evidence in his autosomal DNA he was basal west Eurasian. Raghavan 2013 says there is MA-1 shared more drift(what?) with Native Americans than any people even though they are overwhelmingly east Asian. Is MA-1 still more related to west Eurasians. I really hope they tested whether La Brana-1 is more related to MA-1 than native Americans are.

Laz 2013 says even though some Caucasus people have a lot of MA-1 related ancestry Europeans are still more related because Europeans have much more Loschbour related ancestry and Loschbour shares drift with MA-1 which Stuttgart does not because of her basal Eurasian ancestry.

It seems MA-1 was mainly some form of west Eurasian but his admixture results and PCA placing DOESNT MAKE ANY SENSE.

I doubt there is a lot of Basal Eurasian(who else thinks it is exaggerated?) in the near east because they have the same basic Caucasian skull shape(and many other features) as La Brana-1 and other pre Neolithic Europeans. I bet La Brana-1 and Loschbour would cluster in the same west Eurasian group as modern near easterns if put in a world PCA.

MA-1 was some form of west Eurasian(still have to consider he was a mutt) it makes sense that near eastern ancestry(with basal Eurasian) takes away relatedness to him even if west Eurasian forms native to the near east are more related to MA-1 than WHG is. I don't think Basal Eurasian can always be the answer. I think MA-1 is more related to WHG than to whatever the non basal Eurasian forms of ancestry there is in the near east.

What is MA-1's relatedness to south-central Asians? Was he pure west Eurasian? Could he have been a mixture of many different forms of west Eurasian or unknown forms of Eurasian? I tend to think MA-1 was apart of a group very related to proto WHG.

How do they define MA-1 ancestry if it is so related(or even part proto WHG) to WHG? How do we know MA-1 wasn't a mixture of forms of Eurasian ancestry related to west Eurasian in complicated ways and Basal Eurasian is the whole reason he is more related to WHG than near eastern. There are a lot of possibilities. Wouldn't there have been many different groups in the upper Palaeolithic north Eurasian family besides WHE and ANE?

When is some finally going to get MESOLITHIC OR UPPER PALEOLITHIC GENOMES FROM RUSSIA. That the the key spot that could be where there were types of people related to WHG and ANE or mixed between the two. It could be were Y DNA R1a originated where blonde hair and red hair originated. They may have been the main ancestors of proto Indo Europeans or at least the main people who spread Indo European languages. I don't want anymore from west Europe(Loschbour and la Brana-1 are good enough) only eastern Europe, Balkans, Italy, Siberia, and maybe Scandinavia.

barakobama said...

Eurogenes thread on Raghavan 2013 from November"Rumor has it that the same team of scientists is now trying to sequence genomes from Upper Paleolithic sites west of Mal'ta. I wonder how far west? I see that the authors mention the Sungir site from near Moscow a couple of times in the paper, in relation to its similarity to the Mal'ta site. Perhaps they're working on a Sungir genome right now? If so, what's the bet that the Y-DNA turns out to be another basal R?"

I really hope they are going to get a genome from Dolni Vestonice site in the Czech Republic. The reason is three mtDNA samples taken from that site dating to 31,155ybp two had pre-U5 and one had U8. The pre-U5's mean they are somehow connected to later U5 dominated Mesolithic Europeans. The over 30,000 year old U2 at sungir is apart of an extinct lineage but may have been from the same migration U2e came to Europe.

If Sungir and Mal'ta sites are very similar I do except similar results to MA-1 which is what I don't want. I want to find proto-WHG and prove they are apart of the same major population Mal'ta and AG2 were.

Davidski said...

MA-1, and thus ANE, are basically ancient West Eurasians, which means West Eurasians minus Basal Eurasian admix. Loschbour and La Brana are western versions of the same thing, separated by 16,000 years of genetic drift.

MA-1, AG-2, Loschbour and La Brana are not part East Asian. But they're closer to East Asians than most modern Europeans, because modern Europeans have Basal Eurasian admixture, which pushes them away from other Eurasians, including East Asians.

Native Americans are basically a mix of ancient East Asians and ANE. That's why MA-1 and AG-2 cluster within a cline that runs from Europe to the Americas, and look like mixtures between modern Europeans and Amerindians, and also close to South Central Asians. But if there were more ANE samples on the plot, everything would change, and instead Europeans, West Asians, South Asians and Amerindians would look like mixtures of ANE and other stuff specific to them.

Helgenes50 said...

Knowing that there are 16,000 years between Loschbour and MA-1. Is it logical to
calculate the percentage of the three populations that we share ?( even it's very interesting) EEF WHG and ANE.

it is a little like calculating the percentage between an English a Spanish and a Solutrean
Knowing that the last one can be found in the first one and the second.

it would not make more sense to calculate the average of people living in the same period or almost
like the Swedish farmer and Stuttgart for the farmers and Loschbour and la Brana for the WHG....for example. It's just my opinion

Davidski said...

Yes, I think you're right, but that's all we have at the moment, so it doesn't hurt to speculate. Ancient genomes from different time periods from Eastern Europe will clear everything up, and also maybe expose how naive the three-way EEF/WHG/ANE model was.

DarthVadent2 said...

I have a hypothesis regarding Basal Eurasian, I think one of the earliest populations that carried this component in high frequencies were the Natufians of the Levant. Brace and other anthropologists described them morphologically as having Sub-Saharan African affinities, and they even clustered with African populations, but they didn't conclude that there was any genetic continuity between modern Middle Easterners and the Natufians, but I'm starting to think that they may have been wrong. Both the EEF and Basal Eurasian components exhibit SSA affinities, and Basal Eurasian itself may have been a Northeast African component. So I'm thinking maybe the Natufians, being a pre-agricultural harvesting society, were one of the first carriers of this Basal Eurasian component.

This would also explain the relative African-shift of many Middle Easterners and even some Southern European populations, compared to the more hunter-gatherer influenced WHG+ANE admixed populations of Europe. Even Caucasians, with their high ANE are much closer to Africans than most European populations. Namely because they're mostly descended from Middle Easterners.

Here's what I think, I think there was probably an Ancestral West Eurasian population that was collaterally related to WHG, ANE and the ancestral Non-Basal Eurasian ancestor of EEF. Europeans are basically a mixture of WHG+ANE, while Middle Easterners are a mixture of a population may have been distantly related to WHG and ANE and Basal Eurasian.

About Time said...

@Darth, Yes - with the caveat that all Europeans (even Estonians) are part Basal via EEF. Someone should try to model Basal allele frequencies from the "missing component" of EEF and modern Euros versus WHG/Mal'ta/Ust-Ishim.

Btw, they sure are taking their sweet time with Farmana, Just publish and let's see what's there.