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View Full Version : Using the "fateful traingle" to discover who Euro's non-Yamna ancestors were



Krefter
01-26-2015, 12:14 AM
Through ancient genomes and leaks about an upcoming ancient DNA paper, we can very confidently say that all European's have ancestry from Gok2-Stuttgart like people and theoretical Yamna(25 ANE, 35 WHG, 40 ENF) type people.

In my opinion ANE K8 reveals 3 major truths about the non-Yamna ancestors of Europeans. I'm posting this because some people have been miss lead to believe all European are EEF+Yamna and that all ANE in Europe is due to Yamna-type people.

EEF+YAM+X=modern Europeans. IMO, the best way to find out what X is, is by using ANE K8's fateful triangle PCA(see here (http://bga101.blogspot.com/2014/12/the-fateful-triangle.html)). With Microsoft excel and Microsoft paint, anyone can easily create a fake score and plot it on the ANE K8 fateful triangle.

Here's a spreadsheet of theoretical populations who (Likely)lived in Europe 5,000 years ago, with their ANE K8 scores and coordinates on my Microsoft Paint picture of ANE K8's fateful triangle. The theortical pop's color is in my spreadsheet, so look for a do that is their color.

https://docs.google.com/spreadsheets/d/1exeQlOSvixhVjAHIPXcumJy5DZcRCJ2c2EyDnhdrp0s/edit?usp=sharing

Also here's the key for the fateful triangle(see here (https://drive.google.com/file/d/0B9o3EYTdM8lQREh3dTBFS21FREE/view)), so that you can recognize what dot is who.

1.All European's non-Yamna ancestors(except Balts and far east Euros) had ENF ancestry.

The only Europeans that can be fit as Yam+WHG/ANE are Balts and far eastern Europeans. Meaning all other European's non-Yamna ancestors had ENF ancestry. This leaves room for the possibility that all of Balts non-Yamna ancestors were hunter gatherers from northeastern Europe. This is why I suspect Y DNA N is descended of late Neolithic/Bronze age Baltic hunter gatherers(see here (http://www.anthrogenica.com/showthread.php?3745-Y-DNA-of-Mesolithic-east-Europeans(EHG))).


http://www.anthrogenica.com/attachment.php?attachmentid=3597&stc=1

2.European's non-Yamna ancestors had little or no west Asian ancestry.

It is true that Central and southern Europeans can be fit as Yamna+Gok2+west Asian, but they are far closer to EEF than west Asians. Southwest Europeans are actually clearly mostly EEF. Some southeastern Europeans cluster closest to west Asians and can't be explained as EEF+YAM, which confirms they have recent west Asian ancestry.

http://www.anthrogenica.com/attachment.php?attachmentid=3598&stc=1

3.North European's have Late Neolithic/Bronze age hunter gatherer ancestry from northeast Europe: EEF+YAM can't explain northern Europeans. Even if there was EEF with 60% WHG, most north Euros still need a non-Yamna ancestor who had even more WHG. This also suggests north Euro's non-Yamna ancestors had ANE ancestry, which means they(at least some) lived in northeastern Europe or Scandinavia, because no west European and Balkan(Hungary) genome from before the bronze age published as of far has any ANE ancestry.

http://www.anthrogenica.com/attachment.php?attachmentid=3600&stc=1

Balts actually can't be explained as WHG+YAM or ENF+YAM, meaning their non-Yamna ancestors for sure had ANE ancestry. This is why Balts are not in the WHG/ENF+YAM triangle.

http://www.anthrogenica.com/attachment.php?attachmentid=3596&stc=1

Krefter
01-26-2015, 12:20 AM
It seems unlikely to me that in Britain and Czech two almost identical pops(in terms of ENF-WHG-ANE) were created. I think a Lithuanian or Polish-like population brought Indo European languages to west Europe. This is why on the fateful triangle there is a cline with Basque at one end(least IE) and Lithuanians at the other.

alan
01-26-2015, 01:16 AM
I think there is a good archaeogical case for most north Europeans having some ANE ancestry brought in in the Mesolithic. It seems to correlate with pressure flaked microblades and perhaps also pre-farming pottery. However, neither made it to the isles so there is not a good archaeological case for an ANE Mesolithic wave to the isles. That is a problem because in the isles ANE is highest among the Celtic fringe and so cannot be explained by later Germanic movement etc. In the isles archaeological case for a copper age arrival of ANE is much stronger IMO. It seems to me from the high ANE that the isles main post-Neolithic autosomal flow was distinctly northern European in nature in a modern sense with ANE levels being impossible to explain otherwise. It seems to me that the beaker people who came to the isles were in autosomal terms likely to have pretty much been the same as northern corded ware people. Only something like that can explain the shift IMO.

SwampThing27
01-26-2015, 01:18 AM
It seems unlikely to me that in Britain and Czech two almost identical pops(in terms of ENF-WHG-ANE) were created. I think a Lithuanian or Polish-like population brought Indo European languages to west Europe. This is why on the fateful triangle there is a cline with Basque at one end(least IE) and Lithuanians at the other.

Sorry but could you expand on this. I was always curious why Brits and Czech are so similar in ANE/WHG/ENF, but arent really anywhere near each other geographically.

Chad Rohlfsen
01-26-2015, 01:40 AM
What he is saying is that Corded Ware mixed with other hunters en-route to Northern Europe, or were already less ENF then later Yamnaya upon leaving. That is obvious in the hypothetical Beaker, Corded, and Yamnaya, created by David and myself. 10-15% input from something 80%WHG 20% ANE can cover a lot. Odds are that Neolithic Poles were as much or more WHG than Gok2. It's fairly obvious just looking at the plot. Anyway, the paper will be out soon. With that, David and I will put out models for everyone, with a day or two later.

Chad Rohlfsen
01-26-2015, 01:52 AM
There is a chance that Corded was already less ENF, but we will need the paper with genomes dating between 4000-3000BCE to figure that out. For instance, if a genome between 3000-3500BCE is closer to 30% ENF, then there is no need to look for an additional Baltic or ANE bearing input for Corded Ware. We will have to wait for the paper.

Krefter
01-26-2015, 03:30 AM
What he is saying is that Corded Ware mixed with other hunters en-route to Northern Europe, or were already less ENF then later Yamnaya upon leaving. That is obvious in the hypothetical Beaker, Corded, and Yamnaya, created by David and myself. 10-15% input from something 80%WHG 20% ANE can cover a lot. Odds are that Neolithic Poles were as much or more WHG than Gok2. It's fairly obvious just looking at the plot. Anyway, the paper will be out soon. With that, David and I will put out models for everyone, with a day or two later.

With an oracle? You can get multiple results. Also, we don't know yet exactly what type of west Asian admixture there was.

Chad Rohlfsen
01-26-2015, 03:39 AM
An Oracle is an option, but it will have to be set up a certain way. I will speak with you about that later. What mixture is coming into the steppes won't matter. What will matter is the result there of. If we have a set of Samara samples that stretch from 4500-3000BCE, I can figure it out. I don't want to go over the details on here.

Krefter
01-26-2015, 03:45 AM
An Oracle is an option, but it will have to be set up a certain way. I will speak with you about that later. What mixture is coming into the steppes won't matter. What will matter is the result there of. If we have a set of Samara samples that stretch from 4500-3000BCE, I can figure it out. I don't want to go over the details on here.

What I meant by west Asian, is non-Yamna west Asian. There is obviously recent west Asian ancestry across Europe, and so my point was that has to be in the equation.

Is the Samara paper supposed to be published, soon? Meaning Davidski will have all the genomes ready to analysis?

Chad Rohlfsen
01-26-2015, 03:49 AM
Yes, like I said, the Oracle will be set up in a specific way, with selected populations that are required. I can go over that with you later. Do you mean Polish-like, prior to mixing? I don't totally disagree with that. However, I feel like Bell Beaker is going to be dropped on the Irish/CEU/British area, and possibly more BR1-like, upon entering Britain.

I don't know when the paper or samples will be available.

Krefter
01-26-2015, 04:12 AM
West Euros can be fit as a mix of Polish, Balts, and Scandinavians and something EEF-like, and so there certainly was a Polish or a mixture of pops who combined look Polish, who moved into west Europe in the last 5,000 years. Bell Beaker can't be the only way ANE came to west Europe. BB is a native(WHG-ENF) development anyways, so at some point you got a expect to see a widespread Kurgan culture in west Europe like Hallstatt and La Tene(?)

Chad Rohlfsen
01-26-2015, 04:15 AM
I'm not talking about Iberian BB, but R1b, German Bell Beaker. I don't see any way that R1b is in Iberia by 2800-2700BCE. There is no ANE in El Portalon. That should cover most of the ANE. Yes, there will be some flow from Hallstatt, La Tene, but I don't think that was very high for Britain. I guess that we will have to wait and see.

Chad Rohlfsen
01-26-2015, 04:17 AM
Late Beaker-Tumulus and such, west of the Rhine, for sure. I don't think R1b went far west of the Rhine until around the Bronze Age. 1800BCE in Iberia, for sure. Yes, I do think Bell Beaker is a sort of Pre-Celtic, which is supposed to date to 3000BCE.

Krefter
01-26-2015, 04:26 AM
The only form of Indo European that existed in Iberia, was Celtic, and apparently Celts came there very recently in the Iron age. If Celts only arrived in the British isles in the Iron age to, Bell beaker or some other early wave must be where they get most of their ANE from.

Jean M
01-26-2015, 11:19 AM
The only form of Indo European that existed in Iberia, was Celtic, and apparently Celts came there very recently in the Iron age.

That is what people thought for a long time, but it does not reflect current thinking. You could catch up with present-day thought (and evidence) by reading http://www4.uwm.edu/celtic/ekeltoi/volumes/vol6/6_4/lorrio_zapatero_6_4.html

In brief Iberia has place-names derived from two Pre-Celtic forms of Indo-European as well as Celtic:

1. PIE itself or very close to it. (This was the first wave to arrive in some other parts of Europe too, including the British Isles.)
2. Early Celtic. (Arrived probably in the form of Celtiberian with Late Bell Beaker, and in the NW probably in the Bronze Age.)
3. Ligurian/Lusitanian, similar to Italic. (Presumably derived from Proto-Italo-Celtic. Seems to have arrived from northern Italy via the coast of Southern France in the Bronze Age and settled along the coast right round to what is now Northern Portugal.

Jean M
01-26-2015, 12:20 PM
I don't see any way that R1b is in Iberia by 2800-2700BCE. There is no ANE in El Portalon.

El Portalon is in northern Spain, a long way from the early Copper Age centres of Iberia and the early BB regions. The first copper-prospectors to arrive in Iberia naturally homed in on the copper belts of the south-west. They were not some sort of army sweeping right over the whole of Iberia obliterating all the farmers. Why would they? The farmers were conveniently growing food that the miners could buy in exchange for a copper knife or whatever. I have little doubt that clashes arose eventually between the older farming populations and the various waves of incomers in the Copper and Bronze Ages, but Iberia today is not the end result of a total wipe-out of EEF.

Chad Rohlfsen
01-26-2015, 01:57 PM
El Portalon is in northern Spain, a long way from the early Copper Age centres of Iberia and the early BB regions. The first copper-prospectors to arrive in Iberia naturally homed in on the copper belts of the south-west. They were not some sort of army sweeping right over the whole of Iberia obliterating all the farmers. Why would they? The farmers were conveniently growing food that the miners could buy in exchange for a copper knife or whatever. I have little doubt that clashes arose eventually between the older farming populations and the various waves of incomers in the Copper and Bronze Ages, but Iberia today is not the end result of a total wipe-out of EEF.

El Portalon is not a long ways from surrounding Beaker sites. If R1b had reached Portugal by 2800BCE, then migrated back to Central Europe, should there not be ANE in El Portalon by 2000BCE? That's a lot of dancing around and quite the coincidence if not. There cannot be a group of people that simply do not mix with surrounding locals, failing to distribute ANE for 800 years. Not to mention the Nw African of sw Iberia failing to dispurse out in much of a cline points to a later arrival for me. In other words, they're on the receiving end and not the source.

Jean M
01-26-2015, 04:16 PM
El Portalon is not a long ways from surrounding Beaker sites.

El Portalón is not a Bell Beaker site. There were other people in Iberia in the Copper Age, apart from Bell Beaker. The Bell Beaker people settled patches of Iberia, not all of it. They did not suddenly dispatch the whole farming population of Iberia and replace them. Nor did they necessarily inter-marry with every other group in Iberia.

Plus there were other people who entered at least part(s) of Iberia in the Copper Age who were herders and high in the gene for Lactase Persistence (San Juan Ante Portam Latinam, Spain 3000 BC), who were quite possibly part of a movement from the Balkans ancestral to a component of Basque ancestry.

In short Iberia is not some simple story that you can unravel from one site.

Chad Rohlfsen
01-26-2015, 04:25 PM
El Portalón is not a Bell Beaker site. There were other people in Iberia in the Copper Age, apart from Bell Beaker. The Bell Beaker people settled patches of Iberia, not all of it. They did not suddenly dispatch the whole farming population of Iberia and replace them. Nor did they necessarily inter-marry with every other group in Iberia.

Plus there were other people who entered at least part(s) of Iberia in the Copper Age who were herders and high in the gene for Lactase Persistence (San Juan Ante Portam Latinam, Spain 3000 BC), who were quite possibly part of a movement from the Balkans ancestral to a component of Basque ancestry.

In short Iberia is not some simple story that you can unravel from one site.

I never said it was a Beaker site. It is not simple. However, you still avoid the ANE and NW African issue. How would R1b fail to distribute any ANE and also fail to take in any NW African in SW Iberia. You will have to explain that one.... Plus, R1b is heavier in Northern Spain, and with hardly any NW African affinity.

Jean M
01-26-2015, 05:06 PM
How would R1b fail to take in any NW African in SW Iberia.

NW African? Is this some idea from modern DNA? I certainly suggest (following recent thinking of Iberian archaeologists, plus cattle DNA) that one route of the Neolithic into Iberia was via North Africa, but I doubt whether you could actually distinguish genetically between the people taking this route from those moving along the northern coast of the Mediterranean, except by their Y-DNA, which would be more strongly E.

Obviously today there will be more of a genetic affinity to North Africa in those areas of Iberia (the south) which were captured and held by the Moors in the early Middle Ages.

As for BB in Iberia, we simply have to wait for aDNA. Attempts to argue from modern DNA or non-BB sites is simply a waste of time.

Isidro
01-26-2015, 05:21 PM
It does look to me like ANE in Iberia is a reflux from Scandinavia since it didn't come with the farmers and the West Asian dissipates until dissappearing with the French_Basque and Sardinian.

New conclusions with the autosomal analysis of Kostenki14 drive scientists to minimize invasions from the norm that dictates DNA expansion to the exception and a mosaic of intermixing mega populations is the norm how DNA branches spread around the Globe.Having that into consideration how valid is it to have the populations of Europe limited into only 3 groups.

Chad Rohlfsen
01-26-2015, 06:18 PM
NW African? Is this some idea from modern DNA? I certainly suggest (following recent thinking of Iberian archaeologists, plus cattle DNA) that one route of the Neolithic into Iberia was via North Africa, but I doubt whether you could actually distinguish genetically between the people taking this route from those moving along the northern coast of the Mediterranean, except by their Y-DNA, which would be more strongly E.

Obviously today there will be more of a genetic affinity to North Africa in those areas of Iberia (the south) which were captured and held by the Moors in the early Middle Ages.

As for BB in Iberia, we simply have to wait for aDNA. Attempts to argue from modern DNA or non-BB sites is simply a waste of time.

Actually, this contains Sub-Saharan 1.5-3+% in that region. Which is sorely lacking outside of southern and western Iberia. An expansion of R1b from here doesn't match that.

alan
01-26-2015, 07:23 PM
I think the notion that bell beaker was in general a WHG/ENF mix of native SW Europeans cannot be correct and the isles makes this clear. Certainly by the sort of time beaker was coming to the isles c. 2500-2400BC it really must have been carrying a north European level of ANE. Archaeology would seem to refute the idea that ANE was in the isles in the hunter-gatherers and noone is suggesting farmers brought it. So it does seem that in the isles ANE is a copper/bronze age signal.

The Celtic fringe parts of the Isles are especially high in ANE and the isles in general, metalwork aside, tended to be rather insular in its settlement and burial traits in the Bronze Age. On top of that the Celtic fringe areas were relatively weak in terms of influence of Hallstatt, La Tene etc. So, it does seem to strongly suggest that the pre-Roman population of the isles had received a high ANE input in the copper and very early Bronze ages. That can only mean beaker people and indeed it can only IMO mean that the beaker flow was indeed from areas like the Low Countries which is one of the only strongly beaker areas that is high in ANE and on shores close to the isles.

Whatever happened it is clear that today elevated ANE is a pan-north European thing and the high levels cannot be attributed solely to the Germanic expansions when you look at the levels in the Celtic fringe. Indeed the way NW Europeans cluster together regardless of a Germanic or Celtic background - I am thinking of isles Celts in particular -is very interesting. In western Europe ANE looks very latitude based in terms of its cline while WHG is much less so.

If you looked at this blind of archaeology you would think there had been an east to west thrust across the entirety of northern Europe with little diminishing even when the north-westernmost Celtic fringes were reached. Much of the high ANE zone is within the corded ware zone but the exception is the isles. Its almost as though genetically the people who reached the isles with beakers were very very similar to the Corded Ware people who had reached to the Lower Rhine a century or two before beaker pots came into use there.

Krefter
01-26-2015, 09:44 PM
It does look to me like ANE in Iberia is a reflux from Scandinavia since it didn't come with the farmers and the West Asian dissipates until dissappearing with the French_Basque and Sardinian.

New conclusions with the autosomal analysis of Kostenki14 drive scientists to minimize invasions from the norm that dictates DNA expansion to the exception and a mosaic of intermixing mega populations is the norm how DNA branches spread around the Globe.Having that into consideration how valid is it to have the populations of Europe limited into only 3 groups.

The 3-ancestor thing is the best we have so far. Plus, ANE-WHG-ENF scores can explain middle easterns and Europeans placement in PCAs based on genotype which doesn't assume ANE-WHG-ENF exist, meaning those 3 forms of ancestry are probably very real. Davidski at Eurogenes did not use MA-1 as his ANE reference, he sucked out the non-Han Chinses or east Asian-like ancestry in native Americans. He says ANE is a very robust form of ancestry that is found in America and most of Eurasia, and that it is very easy to estimate percentages of ANE.

vettor
01-31-2015, 01:01 AM
I'm not talking about Iberian BB, but R1b, German Bell Beaker. I don't see any way that R1b is in Iberia by 2800-2700BCE. There is no ANE in El Portalon. That should cover most of the ANE. Yes, there will be some flow from Hallstatt, La Tene, but I don't think that was very high for Britain. I guess that we will have to wait and see.

I hope you are not "aiming" at, saying/targeting, that La Tene and Halstatt belong to north europe instead of central europe!!!!!!!

Chad Rohlfsen
01-31-2015, 03:42 PM
I hope you are not "aiming" at, saying/targeting, that La Tene and Halstatt belong to north europe instead of central europe!!!!!!!

I'm not sure what you're saying here. I'm talking about the spread of ANE to Western Europe. When did I say that they were from Northern Europe?

vettor
01-31-2015, 06:18 PM
I'm not sure what you're saying here. I'm talking about the spread of ANE to Western Europe. When did I say that they were from Northern Europe?

I ask you, is there still a central european concept in regards to ANE or are the central europeans made to be part of northern europeans so that the numbers/calculations can work?
It seems because N1 was found in recent hungarian studies, reich and others need to wave away a concept of central european

Chad Rohlfsen
01-31-2015, 06:21 PM
I ask you, is there still a central european concept in regards to ANE or are the central europeans made to be part of northern europeans so that the numbers/calculations can work?
It seems because N1 was found in recent hungarian studies, reich and others need to wave away a concept of central european

Northern and Central Europeans are similar in ANE numbers. Is that what you mean?

gravetti
01-31-2015, 06:23 PM
Krefter:
"...because no west European and Balkan(Hungary) genome ..."

Krefter,Hungary is not Balkan!

Krefter
01-31-2015, 06:24 PM
Krefter:
"...because no west European and Balkan(Hungary) genome ..."

Krefter,Hungary is not Balkan!

Sure, but it is nearby. I'm not very good with geographic terms.

gravetti
01-31-2015, 06:33 PM
Sure, but it is nearby. I'm not very good with geographic terms.

OK,but this is not only geographic term.It`s cultural and historic as well.

vettor
01-31-2015, 07:19 PM
Northern and Central Europeans are similar in ANE numbers. Is that what you mean?

It seems to me that reich is only linking central to northern because of the affinity of the britsh and czech close genetic relationship. Czech being central europe needs to be renamed to northern european to make the model work in reich's ( or partners) theories.

DMXX
01-31-2015, 09:40 PM
Based on your predicted Yamnaya values, assuming Andronovo were genetically identical and discarding the (currently unquantifiable) potential admixture via the BMAC, what would the extent of contribution by Yamnaya be among various IE-speaking West and South Asian populations, Krefter?

Krefter
01-31-2015, 11:07 PM
Based on your predicted Yamnaya values, assuming Andronovo were genetically identical and discarding the (currently unquantifiable) potential admixture via the BMAC, what would the extent of contribution by Yamnaya be among various IE-speaking West and South Asian populations, Krefter?

I haven't played around with theoretical Yamna and west-south Asians much. The reason is I'm very hesitant about saying we know who the IEs were that spread to west Asia and south Asia and who the people were they mixed with. When I did try to fit Kurds as Yamna and something very southwest Asian, they come out as under 20% Yamna.

DMXX
01-31-2015, 11:51 PM
I haven't played around with theoretical Yamna and west-south Asians much. The reason is I'm very hesitant about saying we know who the IEs were that spread to west Asia and south Asia and who the people were they mixed with. When I did try to fit Kurds as Yamna and something very southwest Asian, they come out as under 20% Yamna.

Agreed. 20% doesn't sound completely off either. I'd be extremely surprised if Yamnaya ancestry in IE West and South Asians exceeds 25%. The genetic constitution of the BMAC is an enigma in itself. They are essentially an eastern oases-centred expansion of early West Asian farming communities. They are likely to be predominantly EEF based on this. Some local hunter-gatherer-fisher settlements were found around South-Central Asia before then, but I have no idea whether their assimilation into these farming communities took place, or to what extent if so. They could be a source of aboriginal ANE in the region, which could make the BMAC folk not that dissimilar to Yamnaya (heavy EEF-ANE) although they'd probably lack WHG.

In any case, based on the linguistic, archaeological and anthropometric data, it is probable the IE waves that spread into West and South Asia were some composite of Andronovo (essentially Yamnaya) and BMAC. If the Kurds are 20% Yamnaya and we assume the 1st millennia B.C. Indo-Iranians were 1/3 BMAC, that'd make the Kurds something like 30% "late" Indo-Iranian genetically.

Krefter
02-01-2015, 12:35 AM
Agreed. 20% doesn't sound completely off either. I'd be extremely surprised if Yamnaya ancestry in IE West and South Asians exceeds 25%. The genetic constitution of the BMAC is an enigma in itself. They are essentially an eastern oases-centred expansion of early West Asian farming communities. They are likely to be predominantly EEF based on this. Some local hunter-gatherer-fisher settlements were found around South-Central Asia before then, but I have no idea whether their assimilation into these farming communities took place, or to what extent if so. They could be a source of aboriginal ANE in the region, which could make the BMAC folk not that dissimilar to Yamnaya (heavy EEF-ANE) although they'd probably lack WHG.

In any case, based on the linguistic, archaeological and anthropometric data, it is probable the IE waves that spread into West and South Asia were some composite of Andronovo (essentially Yamnaya) and BMAC.

I tend to think Indo Iranian languages trace back to the steppe, but I wonder if Armenian and Anatolian are from those Armenian-types(Maykop?). Maybe someone is going to sample genomes related to the origins of IEs in Asia sometime soon.

GailT
02-01-2015, 12:39 AM
I'm trying to keep up with the alphabet soup of refenence genomes or reference populations:

ANE = Ancient North Eurasians related to Upper Paleolithic Siberians
WHG = West European Hunter-Gatherers, who derive from the Upper Paleolithic indigenous population of Europe
EEF = Early European Farmers, who were mainly of Near Eastern origin

What is ENF?

Reich also says that 8000 years ago Russia was inhabited by a distinctive population of eastern European hunter-gatherers with high affinity to a ~24,000 year old Siberian, and "the Yamnaya steppe herders of this time were descended not only from the preceding eastern European hunter-gatherers, but also from a population of Near Eastern ancestry." Was this Near Eastern group the same as EEF? What was the percentage of ANE and WWF in the Yamnaya?

It seems like we need more ancient genomes and more reference populations that can be associated with specifc time periods, and maybe the new paper will provide this. It's very interesting to see the progress but it still seems very imprecise.

Krefter
02-01-2015, 12:47 AM
GailT,

ENF is a name Davidski made up for his "pure" Near eastern component in admixtures ANE K7 and ANE K8. In ANE K8 Stuttgart is 68-72% ENF, and most west Asians have more.

Based on leaks given by Reich I think Mesolithic Russians(aka EHG) were more WHG-like than ANE-like. They were very ANE though, like as much as Native Americans and south Asians. Yamna was a 50/50 mix of Mesolithic Russians(aka EHG) and something similar to Armenians(15% ANE?, rest mostly ENF?).

Me and several other people at Eurogenes think Yamna was 40% ENF, 35% WHG, and 25% ANE, in ANE K8 terms. In Laz's EEF-WHG-ANE test maybe they would be 25% ANE, 55% EEF, and 25% WHG.

vettor
02-01-2015, 01:47 AM
I'm trying to keep up with the alphabet soup of refenence genomes or reference populations:

ANE = Ancient North Eurasians related to Upper Paleolithic Siberians
WHG = West European Hunter-Gatherers, who derive from the Upper Paleolithic indigenous population of Europe
EEF = Early European Farmers, who were mainly of Near Eastern origin

What is ENF?

Reich also says that 8000 years ago Russia was inhabited by a distinctive population of eastern European hunter-gatherers with high affinity to a ~24,000 year old Siberian, and "the Yamnaya steppe herders of this time were descended not only from the preceding eastern European hunter-gatherers, but also from a population of Near Eastern ancestry." Was this Near Eastern group the same as EEF? What was the percentage of ANE and WWF in the Yamnaya?

It seems like we need more ancient genomes and more reference populations that can be associated with specifc time periods, and maybe the new paper will provide this. It's very interesting to see the progress but it still seems very imprecise.

I was told ENF = Eastern Neolithic Farmers ................i.e. pre-EEF

correction --- where EEF is replaced by an Early Neolithic Farmer (ENF) component from the ancient Near East,

Early instead of eastern


read below
http://bga101.blogspot.com.au/2014/09/eurogenes-ane-k7.html
origins seem to be here

Hando
02-01-2015, 12:02 PM
Through ancient genomes and leaks about an upcoming ancient DNA paper, we can very confidently say that all European's have ancestry from Gok2-Stuttgart like people and theoretical Yamna(25 ANE, 35 WHG, 40 ENF) type people.

In my opinion ANE K8 reveals 3 major truths about the non-Yamna ancestors of Europeans. I'm posting this because some people have been miss lead to believe all European are EEF+Yamna and that all ANE in Europe is due to Yamna-type people.

EEF+YAM+X=modern Europeans. IMO, the best way to find out what X is, is by using ANE K8's fateful triangle PCA(see here (http://bga101.blogspot.com/2014/12/the-fateful-triangle.html)). With Microsoft excel and Microsoft paint, anyone can easily create a fake score and plot it on the ANE K8 fateful triangle.

Here's a spreadsheet of theoretical populations who (Likely)lived in Europe 5,000 years ago, with their ANE K8 scores and coordinates on my Microsoft Paint picture of ANE K8's fateful triangle. The theortical pop's color is in my spreadsheet, so look for a do that is their color.

https://docs.google.com/spreadsheets/d/1exeQlOSvixhVjAHIPXcumJy5DZcRCJ2c2EyDnhdrp0s/edit?usp=sharing

Also here's the key for the fateful triangle(see here (https://drive.google.com/file/d/0B9o3EYTdM8lQREh3dTBFS21FREE/view)), so that you can recognize what dot is who.

1.All European's non-Yamna ancestors(except Balts and far east Euros) had ENF ancestry.

The only Europeans that can be fit as Yam+WHG/ANE are Balts and far eastern Europeans. Meaning all other European's non-Yamna ancestors had ENF ancestry. This leaves room for the possibility that all of Balts non-Yamna ancestors were hunter gatherers from northeastern Europe. This is why I suspect Y DNA N is descended of late Neolithic/Bronze age Baltic hunter gatherers(see here (http://www.anthrogenica.com/showthread.php?3745-Y-DNA-of-Mesolithic-east-Europeans(EHG))).


http://www.anthrogenica.com/attachment.php?attachmentid=3597&stc=1

2.European's non-Yamna ancestors had little or no west Asian ancestry.

It is true that Central and southern Europeans can be fit as Yamna+Gok2+west Asian, but they are far closer to EEF than west Asians. Southwest Europeans are actually clearly mostly EEF. Some southeastern Europeans cluster closest to west Asians and can't be explained as EEF+YAM, which confirms they have recent west Asian ancestry.

http://www.anthrogenica.com/attachment.php?attachmentid=3598&stc=1

3.North European's have Late Neolithic/Bronze age hunter gatherer ancestry from northeast Europe: EEF+YAM can't explain northern Europeans. Even if there was EEF with 60% WHG, most north Euros still need a non-Yamna ancestor who had even more WHG. This also suggests north Euro's non-Yamna ancestors had ANE ancestry, which means they(at least some) lived in northeastern Europe or Scandinavia, because no west European and Balkan(Hungary) genome from before the bronze age published as of far has any ANE ancestry.

http://www.anthrogenica.com/attachment.php?attachmentid=3600&stc=1

Balts actually can't be explained as WHG+YAM or ENF+YAM, meaning their non-Yamna ancestors for sure had ANE ancestry. This is why Balts are not in the WHG/ENF+YAM triangle.

http://www.anthrogenica.com/attachment.php?attachmentid=3596&stc=1
So modern North Europeans' have a lot of YDNA N from their Eastern hunter gatherer ancestors?
2)And modern North Europeans also have EEF+YAM too?
And who are North Europeans? Are Germans and Dutch as well as English included?

Hando
02-01-2015, 12:05 PM
What he is saying is that Corded Ware mixed with other hunters en-route to Northern Europe, or were already less ENF then later Yamnaya upon leaving. That is obvious in the hypothetical Beaker, Corded, and Yamnaya, created by David and myself. 10-15% input from something 80%WHG 20% ANE can cover a lot. Odds are that Neolithic Poles were as much or more WHG than Gok2. It's fairly obvious just looking at the plot. Anyway, the paper will be out soon. With that, David and I will put out models for everyone, with a day or two later.

Could you please elaborate by what is this 10%-15%? ENF or WHG?
And what do you mean by "cover a lot"?

Chad Rohlfsen
02-01-2015, 03:58 PM
10-15% additional HG ancestry that probably has ANE. It all depends on the breakdown of Samara at a specific time. We have to wait for the paper.

vettor
02-01-2015, 06:08 PM
And who are North Europeans? Are Germans and Dutch as well as English included?

They use the zones adopted by
Fine-Scale Population Structure in Europe. S. Leslie1, G. Hellenthal2, S. Myers3, P. Donnelly3, 4, International Multiple Sclerosis Genetics Consortium 1) Statistical Genetics, Murdoch Childrens Research Institute, Parkville, Victoria, Australia; 2) University College London Genetics Institute, Darwin Building, Gower Street, London, WC1E 6BT, UK; 3) University of Oxford, Department of Statistics, 1 South Parks Road, Oxford, OX1 3TG, UK; 4) The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK.

so, north of the pyrennes = north european
north of the alps = north european
north of romania, croatia and serbia = north european

so, it seems otzi might be north european if he is austrian or south european if he is italian


The system is basically the same as 23andme use in their model for us


poor central europeans.....missing as usual

DMXX
02-05-2015, 11:36 PM
Since the brief exchange between myself and Krefter here, I've been pondering ways of approximating the genetic input of Yamnaya in the West and South Asian IE speaking populations. There are three issues here:


The absence of aDNA makes all of this entirely speculative to begin with.
Additional complications is a complete information black hole regarding the genetic constitution of intermediary groups that Andronovo-derived populations interacted with (BMAC, aboriginal Central Asian hunter-gatherer-fishers to name but two).
Finally, with respect to ANE, we're confronted with the problem of pre-IE ANE that was no doubt present in both West and South Asia.


Given the above and considering the ANE increase in Europe correlates with Indo-European, I propose that comparing ANE frequencies between various modern South and West Asian IE speaking populations with their non-IE speaking neighbours, and reverse-extrapolating that with Yamnaya, will give us a rough indication of admixture extent. This approach satisfactorily addresses the second (ignoring their contribution and focusing specifically on Yamnaya) and final point (pre-IE ANE is removed).

The above proposition "works" under the following preconditions (with the Pontic-Caspian steppe theory serving as context):

Presumption that the hypothetical Yamnaya deduced by Krefter and fellow enthusiasts at Eurogenes was congruent with derived cultures in the eastern portion (i.e. Sintashta region)
Presumption that Andronovo (Sintashta-derived) is congruent with the above (no significant admixture from local hunter-gatherers around Kazakhstan)
ANE levels were not significantly affected by (likely) admixture with intermediary groups
Neighbouring non-IE speaking groups did not receive significant gene flow from Bronze age IE speakers



This is clearly a hefty set of preconditions. I am under no illusion all four of them will be affirmed with future aDNA results. However, such modelling is necessary to derive meaningful results based on modern population frequencies and a general understanding of archaeology.

Using the Eurogenes K8 population average results (https://docs.google.com/spreadsheets/d/1JVGdg2UsN3jYWgaoxAZu-QsAmuCaq3kT7FvqSXwUsAA/pubhtml) (credit to Longbowman) with Iranians and Kurds, where Assyrians and Iraqi Jews are used as the non-IE speaking neighbours:



Iranian Kurd Assyrian Iraqi_Jewish
19.61 19.31 13.72 12.04

ANE Iranian difference with Assyrian and Iraqi_Jewish = +5.89-7.57%
ANE Kurdish difference with Assyrian and Iraqi_Jewish = +5.59-7.27%


Krefter and other users deduced Yamnaya to be 25% ANE, 40% ENF and 35% WHG (http://www.anthrogenica.com/showthread.php?3694-ANE-K8-oracles-for-Euros-using-ancient-Euros-and-modern-Middle-easterns&p=64065&viewfull=1#post64065). Reverse-engineering the results on the presumption that Yamnaya were 25% ANE provides us with the following estimated admixture ranges:



Yamnaya-like admixture in Iranians = 23.56-30.28%
Yamnaya-like admixture in Kurds = 22.36-29.08%


Recall that, for these numbers to be accurate, at least four preconditions have to be met. I find this to be an unlikely proposition. Also recall these numbers don't take into account the additional admixture gained in South-Central Asia (discussed above), implying the admixture from Bronze age IE speakers among Iranians and Kurds would be greater than the values obtained via direct Yamnaya input alone. Finally, WHG admixture in Asia isn't taken into account here.

In any case, this fun little exercise is nothing more than cerebral wheel-spinning until hard data addressing the three issues of IE admixture in Asia stated in the beginning surface. The values are precisely what I'd expect of Yamnaya admixture in West Asia (it is approximately half (substantially less) of what the less densely populated supra-Carpathian regions of Europe received (http://www.anthrogenica.com/showthread.php?3769-New-Leak-CWC-73-Yamna-modern-North-Euros-50-Yamna)).

I attempted something similar using the Pakistani Pashtuns and the Brahui as their non-IE speaking neighbours, but it appears Davidski dropped them from the later ANE runs. I suspect their Yamnaya admixture range will be several percentages higher than Iranians and Kurds (25-35%?). Afghan Pashtuns and Tajiks will likely be several percentage points higher still (30-40%?).

Have fun mulling over all this, folks!

[Edit]: As for my personal hunches independent of the numbers and above reasoning? 20-30% Yamnaya seems a tad high. I suspect the actual result will be in the 15-20% range for Iranians and Kurds, adding an extra 5-10% for Afghan populations.

Chad Rohlfsen
02-06-2015, 01:36 AM
DMXX,
I don't think that Samara should be used to estimate ancestry into the Near East. I think that those folks were probably more ENF and less WHG, in the Kuban area. Samara is quite far north and the only groups that might come out of there are Corded Ware and maybe Andronovo (via Abashevo). Just looking at the fact that Central Asians have way more WHG than the South Caucasus and Iran, even with them being around half or more East Eurasian. I certainly think that they would've mixed on the way to Kazakstan, as well as with the locals, whom probably already had ENF with the arrival farmers from the south(whom probably had a good chunk of ANE too. Here is my hypothetical breakdown of the West Eurasian part of Kazakhs..

If Yakuts, according to a fairly recent paper, represent the ancestral Turks, then that makes a good starting point. Assuming that the Yakut get a bit of their ANE, all their ENF, and maybe all their WHG from IE expansion to Siberia. I would make the Yakut about 12% ANE and 88% EEur, prior to contact. That would make the West Eurasian part of Kazakhs at about 42%ENF, 25%WHG, 33%ANE. This portion would come out to about 36% of their ancestry, with the remaining 64% the ANE/EEur mix. It does look very much derived from the west and not the south. By way of the fact that there was probably already an ENF/ANE mix, with some WHG already present. Factoring that in, it certainly looks like our Yamnaya mixed with those folks, then Turks came in. WHG is way too high compared to ANE. I don't think it is very probable that the average Kazakh Mesolithic hunter was 40-50%WHG. That seems way too high. I can try to break that down into Yamnaya and local in Kazakhstan.

These are just hypotheticals. No one needs to fall off their rocker...

Krefter
02-06-2015, 03:23 AM
DMXX, I hope you saved your work(Yamna, west Asians) in a file, for future reference and work.

As more is learned about west Asian genetics via modern and ancient DNA, those will be useful notes. Right now I'm going through several thousand mtDNA samples from the Levant and Arabia. It has helped me realize west Asia has been a very diverse place since at least the Neolithic, and has a very much unknown genetic prehistory.

First of all, it's very obvious the maternal lineages in modern (south)west Asians split from EEFs in west Asia a very long time ago, and that in Y DNA and autosomal DNA(high WHG in EEF, lack of ANE) they're pretty distant from each other.

2nd of all, the pop who gave Yamna near eastern ancestry was similar to modern northwest Asians, with high ANE, and low WHG. Not everyone in west Asia was 100% ENF, and I think it's a bit ridiculous some people think that.

3rd of all, near eastern-type mtDNA in Greek Mesolithic hunter gatherers. This could mean we might not be able to distinguish farmer and HG DNA in west Asia.

We don't know all the diff peps who lived in west Asia 1,000sYBP and when you add Yamna to that mix, it becomes very complex and unknown.

jeanL
02-06-2015, 03:42 AM
I would say that some ANE definitely made it to Europe way before the Indo-European people did, namely there will probably be farmers out there with ANE, perhaps not in the upwards of 10%+ but maybe at the level of Basques(i.e 5-6%).

Chad Rohlfsen
02-06-2015, 04:07 AM
JeanL,
If you mean outside of Eastern Europe, plus some Scandinavian and Baltic foragers, this is very unlikely. There was no ANE in Germany, prior to Corded and Beaker folks. None to be seen so far in Iberia, prior to 2000BCE. Maybe some farmers in Eastern Poland, or something, had a trickle. But, maybe not. The only ones almost certainly carrying ANE were this mystery population that mixed into Yamnaya.

Krefter
02-06-2015, 04:44 AM
It's very possible some Neolithic farmer west Asians had ANE. It doesn't seem any made it to Iberia, Germany, and Hungary, because of the wealth of samples from those regions ranging the entire Neolithic. They could have made it to Russia though because Yamna looks like a mix of a northwest Asian-type pop and EHG.

That raises the possibility such people went into other areas of Europe and wherever else. How do we explain Uralics being so similar to Balto-Slavs? A good possibility obviously is because they lived near early IEs and the non-IE ancestors of Balto-Slavs? So maybe the same Armenian-types gave Uralics most of their ENF.

jeanL
02-06-2015, 04:55 AM
JeanL,
If you mean outside of Eastern Europe, plus some Scandinavian and Baltic foragers, this is very unlikely. There was no ANE in Germany, prior to Corded and Beaker folks. None to be seen so far in Iberia, prior to 2000BCE. Maybe some farmers in Eastern Poland, or something, had a trickle. But, maybe not. The only ones almost certainly carrying ANE were this mystery population that mixed into Yamnaya.

How on this Earth can you be so confident about such assertions?? If you could provide something that you are basing such a definite assertion on, I would greatly appreciate it!

Chad Rohlfsen
02-06-2015, 05:09 AM
The various teasers from the paper... No ANE in Spain or Germany, plus a Near Eastern population that is "ANE rich".

jeanL
02-06-2015, 05:25 AM
The various teasers from the paper... No ANE in Spain or Germany, plus a Near Eastern population that is "ANE rich".

Not quite, the teasers say and I quote:

"We show that in western Europe, the farmers of both Germany and Spain >7,000 years ago were descended from a common ancestral stock. These farmers did not replace the earlier hunter-gatherers, but continued to mix with them, leading to a resurgence of hunter-gatherer ancestry in both Germany and Spain ~1,000-2,000 years later. "

Again you are making the inference that this is somewhat translating into no ANE in Spain and Germany based upon Stuttgart having no ANE, however, I cannot come to such conclusions from the statement above, in fact the statement above says nothing about the ANE, it simply mentions the relatedness of the farmers from Spain and Germany. However I would expect for there to differences between such farmers given that both come from different cultures, i.e. Iberia Cardial, Germany LBK. Now this doesn't say anything about the ANE status on the Middle Neolithic farmers, or the Chalcolithic farmers, etc.

Here is another quote from the same abstract:

"However, our analysis of ancient genomes shows that the Ancient North Eurasian ancestry that is ubiquitous in Europe today was rare or absent at the time of the arrival of the Early European Farmers."

Again this is a bit more direct now, but still the words used rare or absent dictate that there was a subset where say ancestry ANE was absent whereas there was another subset where at least one member had ANE making it rare yet not absent.

Krefter
02-06-2015, 05:31 AM
jeanL, the core of what Reich's leak are about is that ANE was brought into much of Europe from Yamna. He has literally said ANE came to Europe from the east in the bronze age. There's a very low chance any of the Neolithic genomes will have signs of ANE. I don't see a reason to debate this, because even if they did have ANE it was very little.

jeanL
02-06-2015, 05:37 AM
jeanL, the core of what Reich's leak are about is that ANE was brought into much of Europe from Yamna. He has literally said ANE came to Europe from the east in the bronze age. There's a very low chance any of the Neolithic genomes will have signs of ANE. I don't see a reason to debate this, because even if they did have ANE it was very little.

Even if little is something that needs to be accounted for, because if say farmers had 5-6% ANE as I mentioned before then the proportions of Yamma ancestry in places like Iberia would be minimal, and it would explain the high levels of Near Eastern.You are asserting that there is a "low"(How low?? Do you know how to quantify it?) chance based on 65 genomes(a lot of which are not from farmers) covering a timespan of 5000 years, and this is assuming that every farmer tested will yield 0% ANE, which is something we don't know right now.

Hando
02-06-2015, 05:39 AM
DMXX, I hope you saved your work(Yamna, west Asians) in a file, for future reference and work.

As more is learned about west Asian genetics via modern and ancient DNA, those will be useful notes. Right now I'm going through several thousand mtDNA samples from the Levant and Arabia. It has helped me realize west Asia has been a very diverse place since at least the Neolithic, and has a very much unknown genetic prehistory.

First of all, it's very obvious the maternal lineages in modern (south)west Asians split from EEFs in west Asia a very long time ago, and that in Y DNA and autosomal DNA(high WHG in EEF, lack of ANE) they're pretty distant from each other.

2nd of all, the pop who gave Yamna near eastern ancestry was similar to modern northwest Asians, with high ANE, and low WHG. Not everyone in west Asia was 100% ENF, and I think it's a bit ridiculous some people think that.

3rd of all, near eastern-type mtDNA in Greek Mesolithic hunter gatherers. This could mean we might not be able to distinguish farmer and HG DNA in west Asia.

We don't know all the diff peps who lived in west Asia 1,000sYBP and when you add Yamna to that mix, it becomes very complex and unknown.
What countries are considered North west Asian? Iran, Armenia, Azerbaijan?

Chad Rohlfsen
02-06-2015, 05:42 AM
There's no ANE in Germany or Spain. I promise you. It's not cryptic. Western and central euro HGs had no ANE.

Krefter
02-06-2015, 05:43 AM
jeanL, this is not something worth debating. When the paper this is going to be forgotten, because none of the farmers will have ANE.

Generalissimo
02-06-2015, 05:47 AM
"However, our analysis of ancient genomes shows that the Ancient North Eurasian ancestry that is ubiquitous in Europe today was rare or absent at the time of the arrival of the Early European Farmers."

Again this is a bit more direct now, but still the words used rare or absent dictate that there was a subset where say ancestry ANE was absent whereas there was another subset where at least one member had ANE making it rare yet not absent.

They're probably referring to Scandinavian hunter-gatherers in that quote, because they had ratios of ANE of 15-19%, but only made up a minority of European hunter-gatherers west of Russia. Hence, rare or absent.

Neolithic farmers moved into Europe via to main routes; the Mediterranean coast and the Danube valley. It's highly unlikely that there was any ANE around the Mediterranean until after the Neolithic, and ancient genomes from Hungary suggest that it didn't get there until the Copper Age at the earliest.

So which Neolithic farmers west of Hungary and south of Sweden could have carried ANE in your opinion? Do you have an archeological culture in mind?

jeanL
02-06-2015, 05:54 AM
Now you guys we are talking about science here, aren't we? I'm glad I'm getting promises, but let's seat back and simply state the obvious which is the whole no ANE in Spain/Germany/etc is pure speculation right now. I'm not saying that there is ANE, I'm saying since we are speculating, I think it is possible to see farmers having low levels(i.e. 5-6%) of ANE, which could have an impact on the evolutionary history of places like Iberia.

vettor
02-06-2015, 05:57 AM
What countries are considered North west Asian? Iran, Armenia, Azerbaijan?

maybe the urals /east side

Generalissimo
02-06-2015, 05:57 AM
Now you guys we are talking about science here, aren't we? I'm glad I'm getting promises, but let's seat back and simply state the obvious which is the whole no ANE in Spain/Germany/etc is pure speculation right now. I'm not saying that there is ANE, I'm saying since we are speculating, I think it is possible to see farmers having low levels(i.e. 5-6%) of ANE, which could have an impact on the evolutionary history of places like Iberia.

But how did you arrive at this assumption that Neolithic farmers from Spain and/or Germany might have carried low levels of ANE, when...

1) Hungarian Neolithic farmers and one Swedish Neolithic farmer did not carry any ANE

2) There's a clear dip today in ANE in southwestern Europe, with some Sardinians showing 0% ANE

jeanL
02-06-2015, 06:02 AM
So which Neolithic farmers west of Hungary and south of Sweden could have carried ANE in your opinion? Do you have an archeological culture in mind?

Man truth be told my knowledge of Central European culture and history isn't anywhere near that of you guys, it isn't news that I'm not a history person, I'm simply going by my observations based on the data seen. As for Hungary, I understand that the genomes except for NE7 and BR2 are mostly 1x coverage, nonetheless I can't find anything about the status(projected or not?) of the ancient genomes on this PCA plot:

http://1.bp.blogspot.com/-xPGV13M4lSM/VEaknJoP-jI/AAAAAAAAJ0I/XmX-S48tr2A/s1600/ncomms6257-f2.jpg

Yes CO1 plots right by Sardinians, now the other folks are more Eastern, Gok4 appears to have more WHG than all the other folks(Sardinians, Otzi, NEs,CO) but less than Basques, yet it seems some of this guys have the same eastward shift in the PC1 direction as Basques do, for example NE2, NE6 and NE3 are all at a higher PC1 level than most Basques. But then again in this very plot we see Bra1 plot way more eastern, which I'm guessing this is the low coverage sequence of it, since bra2 is also included in there.

jeanL
02-06-2015, 06:06 AM
But how did you arrive at this assumption that Neolithic farmers from Spain and/or Germany might have carried low levels of ANE, when...

1) Hungarian Neolithic farmers and one Swedish Neolithic farmer did not carry any ANE

2) There's a clear dip today in ANE in southwestern Europe, with some Sardinians showing 0% ANE

How does the high coverage genome from Hungary score on the K8? I recall you did the analysis on the CO1 genome and it showed no ANE, but how many snps did you use for the run?? I haven't seen any other analysis coming from Hungary. We have Stuttgart, and Gok2 with definitely 0% ANE, Otzi appears also to have 0%. I gotta say I'm surprised Gok2 doesn't show any ANE, that means her WHG was likely of Southern origin and not local SHG, otherwise she would have showed some, although she could have been an outlier, is hard to say based on a single sample.

Generalissimo
02-06-2015, 06:57 AM
How does the high coverage genome from Hungary score on the K8? I recall you did the analysis on the CO1 genome and it showed no ANE, but how many snps did you use for the run?? I haven't seen any other analysis coming from Hungary. We have Stuttgart, and Gok2 with definitely 0% ANE, Otzi appears also to have 0%. I gotta say I'm surprised Gok2 doesn't show any ANE, that means her WHG was likely of Southern origin and not local SHG, otherwise she would have showed some, although she could have been an outlier, is hard to say based on a single sample.

None of the Neolithic genomes from Hungary show any traces of ANE, and they cover a wide period and several cultures.

CO1 might have some ANE judging by some PCA, but if it does, it's only a couple per cent at most, which would make sense, because apparently the late Baden Culture was affected by kurgan migrations. But based on all the data, its ANE looks to be 0% as well.

There are no signals and no indication of ANE in Europe west of Ukraine and south of Sweden prior to the Copper Age.

Generalissimo
02-06-2015, 07:32 AM
Yes CO1 plots right by Sardinians, now the other folks are more Eastern, Gok4 appears to have more WHG than all the other folks(Sardinians, Otzi, NEs,CO) but less than Basques, yet it seems some of this guys have the same eastward shift in the PC1 direction as Basques do, for example NE2, NE6 and NE3 are all at a higher PC1 level than most Basques. But then again in this very plot we see Bra1 plot way more eastern, which I'm guessing this is the low coverage sequence of it, since bra2 is also included in there.

The ancient samples were projected onto that plot, which means that their positions are not 100% true, because they're shifted towards 0 in both axes.

Jean M
02-06-2015, 10:36 AM
Actually, this contains Sub-Saharan 1.5-3+% in that region. Which is sorely lacking outside of southern and western Iberia. An expansion of R1b from here doesn't match that.

The Sub-Saharan African element can be linked to the slave trade organised by the Moors. One study using rolloff investigated the history of sub-Saharan African gene flow into Western Eurasia after after the initial dispersal out of Africa.* It found that almost all Southern Europeans have inherited 1%–3% African ancestry with an average mixture date of around 55 generations ago. That would fit the period of the conquest of much of Iberia by the Umayyad Caliphate (661–750 AD). The Arabs began the slave trade which took so many sub-Saharan Africans into servitude far from home.

This was thousands of years after Bell Beaker.

* Moorjani et al. 2011. The history of African gene flow into southern Europeans, Levantines, and Jews, PLoS Genetics, 7 (4), e1001373.

jeanL
02-06-2015, 02:13 PM
The ancient samples were projected onto that plot, which means that their positions are not 100% true, because they're shifted towards 0 in both axes.

I can't find anything that asserts that on the paper, nonetheless I do see a deviation towards 0,0 coordinates, but then I see that samples such as NE1 are not shifted in the PC1 axis. Also as I said before I find it fascinating that such bold assumptions are made based on a single genome. We know Gok2 has no ANE, we know that the high coverage sequence from Neolithic Hungary likely has no ANE(I hope), yet that translate into: no signals and no indication of ANE in Europe west of Ukraine and south of Sweden before Copper age??? Talking about projections, let get some data points down:

Have you analyzed how many of the Neolithic Hungarian genomes? If so what is the snp count used in each analysis? Also were they run as part of the original thing, i.e. repeat the analysis again or just fit them into the supervised admixture components?

Generalissimo
02-06-2015, 02:20 PM
I can't find anything that asserts that on the paper, nonetheless I do see a deviation towards 0,0 coordinates, but then I see that samples such as NE1 are not shifted in the PC1 axis. Also as I said before I find it fascinating that such bold assumptions are made based on a single genome. We know Gok2 has no ANE, we know that the high coverage sequence from Neolithic Hungary likely has no ANE(I hope), yet that translate into: no signals and no indication of ANE in Europe west of Ukraine and south of Sweden before Copper age??? Talking about projections, let get some data points down:

Have you analyzed how many of the Neolithic Hungarian genomes? If so what is the snp count used in each analysis? Also were they run as part of the original thing, i.e. repeat the analysis again or just fit them into the supervised admixture components?

There's no trace of ANE in any of the genomes with over 100,000 markers apart from MA-1, Motala12, Ajvide58, BR1, BR2, IR1 and the Hinxtons.

If anyone claims that there's ANE among any of the other samples, then they're doing something wrong.

jeanL
02-06-2015, 06:38 PM
There's no trace of ANE in any of the genomes with over 100,000 markers apart from MA-1, Motala12, Ajvide58, BR1, BR2, IR1 and the Hinxtons.

If anyone claims that there's ANE among any of the other samples, then they're doing something wrong.

Which is how many genomes? How many exactly have 100,000 markers?? I can think of Gok2, Otzi, and the high coverage Hungarian Neolithic one, others??

Generalissimo
02-06-2015, 07:25 PM
Which is how many genomes? How many exactly have 100,000 markers?? I can think of Gok2, Otzi, and the high coverage Hungarian Neolithic one, others??

Also well over 100K markers: CO1, KO1, Loschbour, NE5, NE6, NE7, Stuttgart.

You can see how many markers they share with the Mbuti Pygmies from the HGDP/Human Origins and other reference groups here (http://eurogenes.blogspot.com.au/2014/07/shared-drift-stats-between-four-ancient.html).

parasar
02-06-2015, 08:10 PM
There's no trace of ANE in any of the genomes with over 100,000 markers apart from MA-1, Motala12, Ajvide58, BR1, BR2, IR1 and the Hinxtons.

If anyone claims that there's ANE among any of the other samples, then they're doing something wrong.

How much ancestry does Ust-Ishim share with MA-1? Would he land on the mid-top of the triangle?