Teasers: Anatolians of 6300 BC Y DNA G2a, ancestral to EEF

Sile · Sep 15, 2015

bicicleur said:
one could speculate L3f came from Africa along with R1b-V88 8000 years ago, and that R1b-V88 was detected at Els Trocs

Spain Els Trocs [Troc3] M 5178-5066 BC R1b1c M415+, M343+, [L754 equivalent: L774/PF6245/YSC277+, PF1144+, V88 eqivalent: PF6376+] M478-, PF6399-, L265-, L150-, M269-, V35-, V69- R1b1c(xR1b1c2, R1b1c3) pre-T2c1d2 Haak 2015; personal comm Sergey Malyshev, review of Y-DNA raw data

on the other hand, wasn't there E-M81 in Asturias, which couldn't be Moorish
and TMRCA for E-M81 is just 2100 years

maybe E-81

latest paper

http://www.ncbi.nlm.nih.gov/pubmed/25677690

Am J Phys Anthropol. 2015 Jun;157(2):242-51. doi: 10.1002/ajpa.22705. Epub 2015 Feb 11.
Paternal lineages in Libya inferred from Y-chromosome haplogroups.
Triki-Fendri S1, Sánchez-Diz P2, Rey-González D2, Ayadi I1, Carracedo Á2,3, Rebai A1.
Author information
Abstract

Many studies based on genetic diversity of North African populations have contributed to elucidate the modelling of the genetic landscape in this region. North Africa is considered as a distinct spatial-temporal entity on geographic, archaeological, and historical grounds, which has undergone the influence of different human migrations along its shaping. For instance, Libya, a North African country, was first inhabited by Berbers and then colonized by a variety of ethnic groups like Phoenicians, Greeks, Romans, Arabs and, in recent times, Italians. In this study, we contribute to clarify the genetic variation of Libya and consequently, of North African modern populations, by the study of Libyan male lineages. A total of 22 Y-chromosome-specific SNPs were genotyped in a sample of 175 Libyan males, allowing the characterization of 18 Y-chromosomal haplogroups. The obtained data revealed a predominant Northwest African component represented by haplogroup E-M81 (33.7%) followed by J(xJ1a,J2)-M304 (27.4%), which is postulated to have a Middle Eastern origin. The comparative study with other populations (∼5,400 individuals from North Africa, Middle East, Sub-Saharan Africa, and Europe) revealed a general genetic homogeneity among North African populations (FST = 5.3 %; P-value < 0.0001). Overall, the Y-haplogroup diversity in Libya and in North Africa is characterized by two genetic components. The first signature is typical of Berber-speaking people (E-M81), the autochthonous inhabitants, whereas the second is (J(xJ1a,J2)-M304), originating from Arabic populations. This is in agreement with the hypothesis of an Arabic expansion from the Middle East, shaping the North African genetic landscape.

© 2015 Wiley Periodicals, Inc.

Arame · Sep 15, 2015

The situation of the Europeans reaching the Americas is completely different because the two groups had been genetically separated for over 15,000 years and they evolved in completely different natural environments during that time, exposed to different microbes. In Eurasia all populations constantly had some sort of contact with their immediate neighbours

Of course there was contacts in Eurasia, but that contacts are not sufficient to have the same level of immunity all across Eurasia. The best example is the Black Death that decimated the half of medieval European population. There was other cases in Late antiquity in Near East.

Anyway, if immunity played any role in "wiping out" Neolithic lineages, it should have affected both paternal and maternal lineages, which isn't the case at all.

Exact. But when the epidemy ends women have better chances to transmit their genes than the males. They can become the concubine of new males etc etc. Modern Mexicans and Venezuelans large have number of native mtDNA. But they have high European Y DNA.

My point is that what happened in Europe was special and all that can't be explained by wars and killings.
For example we don't see such mass replacement of Y DNA among southern IEs ( Indians, Iranians, Armenians and Greeks ). So it is possible that the European neolithic population density also played a role.

And of course there is the question of autosomal genetics. I think there are some not well understood phenomens with autosoms that we don't take into account. The so called "native ancestry resurgence".
It's my opinion it could be wrong but I think in the long run the alleles that are adapted to a specific climatic and regional conditions are favoured, and the 'alien' genes or alleles that creates incompatibilities with the others genes functioning are removed. In the long run we get something like Basques with so high ANE related R1b but with native autosoms.

epoch · Sep 15, 2015

Sile said:
no....the goal is to check if the 6300BC anatolian farmers are compatible with the central european farmers belonging to LBK_EN

it has nothing to do with hunters or any markers that exceed thousands of years from these Anatolians

Wait. I was referring to the CB13 paper. Not the El Portalon paper. Perhaps I am confused, but to my best knowledge that was the one that tried to find where EEF got its WHG admixture.

From the paper itself:

D-statistics
Using the 1000 Genomes reference dataset, we computed D-statistics (Durand et al. 2011) of the form D (Hunter-gatherer1, Hunter-gatherer2; Neolithic farmer; Outgroup) to test whether any Neolithic farmer, including CB13 Cardial sample, is closer to one of the two hunter-gatherers (Fig.4 and Table S10). Standard errors were computed using a weighted block jackknife approach (Busing et al. 1999) over 5 Mb blocks

http://mbe.oxfordjournals.org/content/early/2015/09/02/molbev.msv181.full.pdf+html

bicicleur 2 · Sep 15, 2015

epoch said:
No, it doesn't: The goal was to check the affinity famers had with different known HG's, in order to see which is most likely the source of the WHG admixture. The fact that KO1 was contemporary to neolithic could be influential, though. Perhaps KO1 was slightly admixted with farmers.

the D stats compare KO1 with Motala 12, Loschbour and La Brana.

it could be KO1 is slightly less WHG then Motala 12, Loschbour and La Brana but still WHG

Gökhem Västergötland [regional TRB]

Sweden

Gok4

M

4-5 ka

I2a1b1 L161.1 xS2639

Genetiker 1+ 0 – op 35 onzeker

Pitted Ware	Sweden	Ajvide [Ajv 52]	M	3000-2400 BC 4,75 ka	I2a1a2a1-L1287 xL233	Genetiker 2+ 5- op 82 I, I2, I2a en I2a1 onzeker
Pitted Ware	Sweden	Ajvide [Ajv 58]	M	2800-2000 BC 4,75 ka	I2a1 I2a1a2a1-L1287 xL233	Genetiker 18+ 36- op 82	M429+, P126+, P129+, L460+, P37.2+	U4d	Skoglund 2014
Pitted Ware	Sweden	Ajvide [Ajv 59]	M	2800-2000 BC 4,75 ka	I-M170	Genetiker 1+ 0- op 149 onzeker		U	Skoglund 2014
Pitted Ware	Sweden	Ajvide [Ajv 70]	M	2800-2000 BC 4,75 ka	I2a1a2a1-L1287 xL233	Genetiker 1+ 11- op 82 onzeker		U4	Malmstrom 2009; Skoglund 2012; Brandt 2013;Skoglund 2014
Pitted Ware	Sweden	Ire, Hangvar, Gotland [Ire 8]	M	2800-2000 BC 4,5 ka	I2a1b1a1-S2703 L1498+ S2703 = Y3749 xY3722	Genetiker Y3749 2+ 0- op 5 onzeker		U4d	Malmstrom 2009;Skoglund 2012; Brandt 2013; Skoglund 2014; Malmstrom 2015

Sweden

Stora Förvar 11

M

7,5 ka

I1-M253

Genetiker 7+ 10 – op 301

all with low coverage
AJV58 has best coverage of them
don't know anything about Gök2

Arame · Sep 15, 2015

War is not a one sided thing. With more or less equal technology the invading male has approximatively the same chances to be killed than to kill. All that history from antiquity to medieval time show that wars don't change much the Y DNA frequency. Of course it change but no so dramatically as in the case of Western European R1b.

It is possible to explain that by pacifist matriarchal societies but I don't think it will work. There are cases of violence and killings at Late Neolithic. The Neolithic Europe before IE was not the pacifist society that we imagine and certainly they did know what is the war.

epoch · Sep 15, 2015

Angela said:
I think it's probably the case, as I've previously proposed, that WHG in Europe is descended from a hunter-gatherer population that existed in the Near East.

Of course, the migration of these hunter-gatherers into Europe would have been before the LGM, so there was plenty of time for WHG to undergo a lot of drift.

O dear. I think I misunderstood you, in that I assumed you were arguing the WHG *component* in current day Europe descended from EEF/ANE. But you seem to argue that mesolithic and UP HGs came from the near east. Sorry for that.

K14 is interesting in that respect. But IIRC Razib Kahn mentioned that WHG was more related to Asians than to EEF.

Angela · Sep 15, 2015

epoch said:
O dear. I think I misunderstood you, in that I assumed you were arguing the WHG *component* in current day Europe descended from EEF/ANE. But you seem to argue that mesolithic and UP HGs came from the near east. Sorry for that.

K14 is interesting in that respect. But IIRC Razib Kahn mentioned that WHG was more related to Asians than to EEF.

No, no, I didn't mean that. Or, yes, yes, you misunderstood me. Let's just say we got our wires crossed.

What I was talking about is the fact that in the Lazaridis et al paper the authors said that their statistical analysis showed that EEF (Stuttgart) seemed to contain anywhere from a couple of percent to 40% WHG. They further said that this "WHG" component in the EEF was likely picked up on the way into Europe (the Balkans) or in Central Europe itself. However, they also said that they doubted either extreme, but that only an ancient farmer genome from the Near East would settle the matter, because their calculations were based on using the Bedouin as a proxy (as Allentoft did after them, along with a lot of bloggers.)

You can find all this starting on page 59 of the Lazaridis et al paper.
http://www.nature.com/nature/journal/v513/n7518/full/nature13673.html

Now, I think I recall that somewhere else in their paper they settled for a "best guess" of around 20%, but don't hold me to that because I don't have the reference, and I don't have the time right now to read the almost 200 pages again. Certainly, however, a figure of around 25% is what the bloggers were using, and using to posit extremely high "WHG" figures in the European Neolithic farmers.

Now we have this abstract of the new Lazaridis paper from the Reich Lab seemingly saying that the Early European farmers are virtually identical to the Anatolian Neolithic farmers. So, what to make of this?

Clearly, there wasn't any picking up of any WHG in the Balkans or Central Europe. (That isn't to say some wasn't picked up from around the Middle Neolithic period, about which more later.)

So, what is the composition of these homogeneous Near Eastern Farmers? Do they still seemingly share a component with the WHG of Europe? How much is it? What was the direction of gene flow?

Did the WHG at some point migrate to parts of the Near East? I'm not aware of any such possible early movement, but I suppose it's possible. Europe is usually a sink for gene flow.

Or, was the gene flow going in the other direction? In considering that, with what movements could we connect it? Well, there are a couple of papers that suggest that the Gravettian, thousands of years before, moved from the greater Near East to Europe.(That's discussed on a thread here, with the relevant citations.) IF that were the case, then we might have a situation where the "WHG" in Europe are distantly removed and drifted descendants of hunter-gatherers from the Near East. That might explain the "WHG-LIKE" partial signal they were picking up in Stuttgart.

That's what I meant.

We'll have to wait for the paper to see how they explain it all.

Oh, and I'd like an update about "Basal Eurasian" please.

Were there two groups (or more) of hunter gatherers in the Near East, one distantly related to the WHG of Europe, and one from the early "split" in the OOA population, i.le the "Basal Eurasian"hunter-gatherers?
Did one group of these hunter-gatherers invent agriculture and animal domestication and then merge with the other group, or did they merge and then invent agriculture?

It seems that some people would like there to be real, discernible substructure, with the Natufians being the Basal Eurasian group that invented agriculture, and the "other" hunter-gatherers, the ones "related" to WHG, being absorbed later. Maybe then it would show that EEF doesn't equal ENF, and that those ENF numbers might have some validity as representing the Natufians? I don't know. I don't see how it matters in the long run. The point is that we now know, I think, that the EEF number represents the percentage of total ancestry in modern Europeans that can be attributed to Near Eastern farmers who arrived in Europe after about 7000 BC.

I do remember seeing a statement from Patterson somewhere to the effect that the admixing had been going on for so many thousands of years that it was difficult to detect substructure, or something like that, but maybe I'm misremembering, or maybe they've changed their minds. We'll soon know.

Angela · Sep 15, 2015

I just wanted to address this issue of the numbers for "EEF" "EN" in various charts, maps etc.

This is the original 3 Population Table from Lazaridis et al:

View attachment 7417

This is the table of Early Neolithic (in Europe)/WHG/Yamnaya: (Same authors)

It's very apparent that the "farmer" numbers, roughly speaking, have changed. Does that mean that the first chart is "wrong" now? I don't think that's necessarily so, although a little clarification from the authors would be nice.

Looking at the Haak table, can we interpret it as saying that the EN figure here (based on LBK) strictly represents not just those people who left for Europe from Anatolia/Northern Levant around 7000 BC (and continuing gene flow), but actually what remains of those people in modern Europeans after subsequent migrations?

It was said in Haak that Yamnaya could be modeled as half " MODERN Armenian like". I don't know how much WHG Modern Armenians have, but I doubt they have much. They have quite a bit of ANE, I would think. The rest, however, is "farmer" ancestry, is it not? (I think we're going to have to wait for the Reich Lab analysis of Near Easterners to get some real clarity.)

So, does the "EEF" number from Lazaridis et al represent the specifically LBK type ancestry remaining in Europeans PLUS the "eastern" farmer ancestry which went into the ethnogenesis of Yamnaya?

@Tomenable

If this new Lazaridis et al paper says what we think it will say, then any map with an "EEF" figure based on subtracting supposedly "WHG" ancestry from the Lazaridis et al EEF percentage is just flat out wrong. (which I said at the time, not that anyone listened.

)

If someone wants to make a map of EEF they should use the numbers in the Lazaridis et al paper. You can't use the blogger "estimates" which have now been proved wrong, or even some combination of the Lazaridis et al figures and the blogger figures, because they are measuring two different things.

Or, someone could make a trio of maps based on the Haak et al paper, with some sort of note that the EN number doesn't represent all the Near Eastern farmer ancestry in Europeans.

Ed. Another more minor problem is that the divide in Spain is in no way that far south. Spain North in Lazaridis et al's list of populations is Pais Vasco, so virtually all of Spain should get the population figures listed under "Spain".

Angela · Sep 15, 2015

It used to be thought that the Gravettian grew out of the Aurignacian:
http://www.academia.edu/3164654/The...d_I_Human_Migrations_and_the_Changing_Climate

More recent thinking (2007)sees it as a new flow of people, but what I have been able to find is papers that see it as an outgrowth of the Ahmarian culture of the eastern Mediterranean. Interestingly, the area on the maps corresponds to the Levant, southern Anatolia.
http://paleo.revues.org/607

If someone has a site for a paper positing an origin in the Caucasus and thus a migration flow from north of it and then west into Europe I'd love to see it.

epoch · Sep 15, 2015

Angela said:
No, no, I didn't mean that. Or, yes, yes, you misunderstood me. Let's just say we got our wires crossed.

What I was talking about is the fact that in the Lazaridis et al paper the authors said that their statistical analysis showed that EEF (Stuttgart) seemed to contain anywhere from a couple of percent to 40% WHG. They further said that this "WHG" component in the EEF was likely picked up on the way into Europe (the Balkans) or in Central Europe itself. However, they also said that they doubted either extreme, but that only an ancient farmer genome from the Near East would settle the matter, because their calculations were based on using the Bedouin as a proxy (as Allentoft did after them, along with a lot of bloggers.)

You can find all this starting on page 59 of the Lazaridis et al paper.
http://www.nature.com/nature/journal/v513/n7518/full/nature13673.html

Now, I think I recall that somewhere else in their paper they settled for a "best guess" of around 20%, but don't hold me to that because I don't have the reference, and I don't have the time right now to read the almost 200 pages again. Certainly, however, a figure of around 25% is what the bloggers were using, and using to posit extremely high "WHG" figures in the European Neolithic farmers.

Didn't they mention the more WHG they assume in EEF, the more Sub-Saharan admixture they had to assume in Bedouin? I don't really get this. Others have assumed African admixture in BE, on the basis that TreeMix sometimes comes up with that, if I may quote from memory. But I have seen TreeMix runs where admixture from EEF to Mbuti is assumed. That is seriously strange. I can understand backflow to Africa, but to Pygmee's? They are supposed to have forked ages ago from Bantu's.

What if Basal Eurasian is an far earlier human wave out of Africa than WHG/Part of EEF/East Asians? They could even be something like these:
https://en.wikipedia.org/wiki/Skhul_and_Qafzeh_hominids

If you add Neanderthals to admixture runs without aloowing them to become a separate instance they look all African. That is because they share ancestral DNA with Africans that are derived or drifted in the OoA bunch.

O, look at some of K=20 admixture runs where Bedouin becomes a separate instance. All of a sudden WHG in EEF goes up, and oddly enough, Loschbour starts having a EEF component.

Angela said:
Now we have this abstract of the new Lazaridis paper from the Reich Lab seemingly saying that the Early European farmers are virtually identical to the Anatolian Neolithic farmers. So, what to make of this?

Clearly, there wasn't any picking up of any WHG in the Balkans or Central Europe. (That isn't to say some wasn't picked up from around the Middle Neolithic period, about which more later.)

So, what is the composition of these homogeneous Near Eastern Farmers? Do they still seemingly share a component with the WHG of Europe? How much is it? What was the direction of gene flow?

Did the WHG at some point migrate to parts of the Near East? I'm not aware of any such possible early movement, but I suppose it's possible. Europe is usually a sink for gene flow.

Or, was the gene flow going in the other direction? In considering that, with what movements could we connect it? Well, there are a couple of papers that suggest that the Gravettian, thousands of years before, moved from the greater Near East to Europe.(That's discussed on a thread here, with the relevant citations.) IF that were the case, then we might have a situation where the "WHG" in Europe are distantly removed and drifted descendants of hunter-gatherers from the Near East. That might explain the "WHG-LIKE" partial signal they were picking up in Stuttgart.

That's what I meant.

We'll have to wait for the paper to see how they explain it all.

Couldn't Kostenki 14's EEF component be interesting in this regard? Here is a man that already carries both components.

Angela said:
Oh, and I'd like an update about "Basal Eurasian" please. Were there two groups (or more) of hunter gatherers in the Near East, one distantly related to the WHG of Europe, and one from the early "split" in the OOA population, i.le the "Basal Eurasian"hunter-gatherers?
Did one group of these hunter-gatherers invent agriculture and animal domestication and then merge with the other group, or did they merge and then invent agriculture?

It seems that some people would like there to be real, discernible substructure, with the Natufians being the Basal Eurasian group that invented agriculture, and the "other" hunter-gatherers, the ones "related" to WHG, being absorbed later. Maybe then it would show that EEF doesn't equal ENF, and that those ENF numbers might have some validity as representing the Natufians? I don't know. I don't see how it matters in the long run. The point is that we now know, I think, that the EEF number represents the percentage of total ancestry in modern Europeans that can be attributed to Near Eastern farmers who arrived in Europe after about 7000 BC.

I do remember seeing a statement from Patterson somewhere to the effect that the admixing had been going on for so many thousands of years that it was difficult to detect substructure, or something like that, but maybe I'm misremembering, or maybe they've changed their minds. We'll soon know.

The Natufians are in the right place (Israel), doing the right thing (Harvesting wild cereals) at the right time.

epoch · Sep 15, 2015

@Angela

The upper paleolithic samples we have seen are strange too. We have a few which have clear affinity with Europeans, to wit Mal'ta, K14 and Afontova Gora 2. All three of them carry components present in current day Europeans. And we have two that appear to have little clear affinity to Europeans: Ust Ishim and Oase 2. The latter are considered "dead ends" by a number of people, for whatever reason. K14 is considered an admixture that didn't have any influence in Europeans as we consider EEF to be of later date.

So only the most eastern two are considered somewhat ancestral to Europeans. That does seem rather odd.

EDIT: I think a number of upper paleolithic samples are to be investigated, under which the famous Red Lady of Paviland (despite his name a man). So we may find more interesting stuff.

Angela · Sep 15, 2015

Epoch:
Didn't they mention the more WHG they assume in EEF, the more Sub-Saharan admixture they had to assume in Bedouin? I don't really get this. Others have assumed African admixture in BE, on the basis that TreeMix sometimes comes up with that, if I may quote from memory. But I have seen TreeMix runs where admixture from EEF to Mbuti is assumed. That is seriously strange. I can understand backflow to Africa, but to Pygmee's? They are supposed to have forked ages ago from Bantu's.

I'm not totally clear on it either, which is why I hope they clarify things in the paper. That's also my recollection of what they said, for what it's worth.

Are you referring to the paper that showed EEF in the San? I don't have the paper at my fingertips but from what I recall it's been demonstrated that there is evidence of more recent gene flow from East African "farmers" into them. It's sort of like the situation with some very isolated, presumed "pure" Amazonian Indians who wind up having some small amounts of "European". Didn't one paper also show some much more recent East Asian in one isolated tribe, and the researchers can't figure out how it got to them? There are absolutely no "pure" groups anymore.

Anyway, to the best of my recollection the paper posited a flow from the Near East into the populations of East Africa then many years later with another major migration trickling into the San. That was just talking about post Neolithic gene flow. Recent papers just dealing with yDna "E" clades show the same thing. Maybe gene flow north, but then a stay in the southern Levant for a while, then a flow back down to the Horn where new clades are born, then that moving south and southwest. That's without considering that perhaps it was DE that moved out of Africa, with a split out of Africa, and then E going back to Africa and then the back and forth described above starting.

What if Basal Eurasian is an far earlier human wave out of Africa than WHG/Part of EEF/East Asians? They could even be something like these:
https://en.wikipedia.org/wiki/Skhul_and_Qafzeh_hominids

That might be what Lazaridis et al had in mind as a possible explanation.

O, look at some of K=20 admixture runs where Bedouin becomes a separate instance. All of a sudden WHG in EEF goes up, and oddly enough, Loschbour starts having a EEF component.

It just might turn out that whatever admixtures took place that far back in pre-history just can't be parsed out mathematically the way that somepeople had hoped. I'd be happy to get some clarity for events starting from the late Mesolithic.

One thing that's clear, however, is that the Bedouin weren't a good proxy.

Couldn't Kostenki 14's EEF component be interesting in this regard? Here is a man that already carries both components.

I think it might prove that when you have genomes that are that old, that far back in the tree, there are going to be correlations and similarities to all of us.

The Natufians are in the right place (Israel), doing the right thing (Harvesting wild cereals) at the right time.

Yes, they are and some scholars believe they were probably the first farmers as well:
http://www.columbia.edu/itc/anthropology/v1007/baryo.pdfbut not all scholars believe that they were necessarily the first to do so; some papers say that this was going on in the foothills of the Euphrates either contemporaneously or perhaps even earlier.

However, by 2010, the same author was having doubts that they actually were the first to domesticate grains. See Michael Balter: The Tangle Web of Agriculture:
https://www.google.com/webhp?ie=utf-8&oe=utf-8#q=Michael+Balter:+The+Tangled+Roots+of+Agriculture

Plant cultivation, which is different from plant foraging, is also different from plant "domestication":
http://www.academia.edu/1529206/Evi..._and_Domestication_in_the_Neolithic_Near_East

One of the sites where the earliest signs of tilling (plant cultivation) have been found is Tell Abu Hureyah in far northern Syria:
https://en.wikipedia.org/wiki/Tell_Abu_Hureyra

There are signs in the Levant as well, but they're later.

I could go on, but you get the point. It's by no means clear that the Natufians were the first "farmers" or even that the first farmers are necessarily descended from the Natufians.

Sile · Sep 15, 2015

Angela said:
I just wanted to address this issue of the numbers for "EEF" "EN" in various charts, maps etc.

This is the original 3 Population Table from Lazaridis et al:

View attachment 7417

This is the table of Early Neolithic (in Europe)/WHG/Yamnaya: (Same authors)

It's very apparent that the "farmer" numbers, roughly speaking, have changed. Does that mean that the first chart is "wrong" now? I don't think that's necessarily so, although a little clarification from the authors would be nice.

Looking at the Haak table, can we interpret it as saying that the EN figure here (based on LBK) strictly represents not just those people who left for Europe from Anatolia/Northern Levant around 7000 BC (and continuing gene flow), but actually what remains of those people in modern Europeans after subsequent migrations?

It was said in Haak that Yamnaya could be modeled as half " MODERN Armenian like". I don't know how much WHG Modern Armenians have, but I doubt they have much. They have quite a bit of ANE, I would think. The rest, however, is "farmer" ancestry, is it not? (I think we're going to have to wait for the Reich Lab analysis of Near Easterners to get some real clarity.)

So, does the "EEF" number from Lazaridis et al represent the specifically LBK type ancestry remaining in Europeans PLUS the "eastern" farmer ancestry which went into the ethnogenesis of Yamnaya?

@Tomenable

If this new Lazaridis et al paper says what we think it will say, then any map with an "EEF" figure based on subtracting supposedly "WHG" ancestry from the Lazaridis et al EEF percentage is just flat out wrong. (which I said at the time, not that anyone listened. )

If someone wants to make a map of EEF they should use the numbers in the Lazaridis et al paper. You can't use the blogger "estimates" which have now been proved wrong, or even some combination of the Lazaridis et al figures and the blogger figures, because they are measuring two different things.

Or, someone could make a trio of maps based on the Haak et al paper, with some sort of note that the EN number doesn't represent all the Near Eastern farmer ancestry in Europeans.

http://open-genomes.org/images/P5A%20with%20migrations.png

the armenians began in the map as AMUQ B lands.....basically where modern turkey meets syria on the meditteraen

you can read other information on these ancient "armenian" archeology in AMUQ ( Cicilia )

the logical answer is that htese 6300BC NW Anatolians farmed from this anatolian lands to central german lands and the the later hungarian samples was due to hunters arriving into hungarian lands via the steppe

Angela · Sep 15, 2015

There is another interesting paper that will be presented at the ASHG conference:

[h=3]Ancient European haplotype enrichment in modern Eurasian populations.[/h] Authors:
D. Harris¹; T. O’Connor²

Institutes
1) Graduate Program in Molecular Medicine, University of Maryland School of Medicine, Baltimore, MD; 2) Institute for Genome Sciences, Program in Personalized and Genomic Medicine, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD.

"Abstract:
The diversification of modern European populations is a fascinating puzzle that has recently advanced due to the sequencing of ancient European genomes. We analyzed 732 modern West Eurasian individuals using three ancient samples coming from the Lazardis et al. Human Origins Array dataset. Specifically, we determined ancient European haplotype enrichment by calculating pairwise differences (PWD) between each ancient European individual and modern Western Eurasian individuals in 50 SNP blocks. Modern Western Eurasians had the fewest PWD across all population groups with the farming Stuttgart individual and had the most PWD with the Loschbour and Motala12 hunter-gatherer individuals confirming Lazardis et al. observation that modern Europeans are more similarly related to ancient individuals coming from a farming community. We selected SNP blocks, for gene ontology enrichment analysis through the use of GORILLA, based on 1) the 10% of regions with greatest differences of PWD between groups, and 2) the 10% of those regions from the first criterion that most closely correlated with the geography of those groups. Most SNP blocks positively correlated to PC1 (latitude) and PC2 (longitude), therefore we focused on outliers that negatively correlated to biogeography. For SNP blocks that negatively correlated to PC1; “regulation of chondrocyte development”, “androsterone dehydrogenase activity”, and “antigen processing and presentation of endogenous peptide antigen” had the highest enrichment score in the comparison of the Stuttgart, Loschbour, and Motala12 individuals, respectively. Interestingly, the “alpha-beta T cell receptor complex” and “interleukin-17 receptor activity” (including CD3D,E,G and IL17RC,E) were enriched in the Loschbour and Motala12 comparisons of SNP blocks that were positively correlated to PC2. In addition, the Stuttgart individual had the lowest PWD disparity between all modern populations for the SNP blocks that contain the IL17R and CD3 genes, which potentially indicates selection acting on these immune system haplotypes from the Stuttgart individual consistent with the Stuttgart farmer and modern Europeans’ continual close interaction with animals and zoonotic disease exposure. In conclusion, our approach of calculating PWD in small SNP blocks supported prior conclusions made by Lazardis et al. and illuminated small genomic haplotypes that are of importance to the evolution of modern West Eurasian populations."

It looks like selection for genes found in Stuttgart to me.

epoch · Sep 15, 2015

Angela said:
It looks like selection for genes found in Stuttgart to me.

Yes. No matter what our descent is made off, we live in the environment more similar to Stuttgart rather than Loschbour.

epoch · Sep 15, 2015

Angela said:
Are you referring to the paper that showed EEF in the San? I don't have the paper at my fingertips but from what I recall it's been demonstrated that there is evidence of more recent gene flow from East African "farmers" into them. It's sort of like the situation with some very isolated, presumed "pure" Amazonian Indians who wind up having some small amounts of "European". Didn't one paper also show some much more recent East Asian in one isolated tribe, and the researchers can't figure out how it got to them? There are absolutely no "pure" groups anymore.

Anyway, to the best of my recollection the paper posited a flow from the Near East into the populations of East Africa then many years later with another major migration trickling into the San. That was just talking about post Neolithic gene flow. Recent papers just dealing with yDna "E" clades show the same thing. Maybe gene flow north, but then a stay in the southern Levant for a while, then a flow back down to the Horn where new clades are born, then that moving south and southwest. That's without considering that perhaps it was DE that moved out of Africa, with a split out of Africa, and then E going back to Africa and then the back and forth described above starting.

I was referring to something different, can't exactly remember where I saw it, but your paper may be this: http://arxiv.org/abs/1307.8014
Discussed at Dienekes: http://dienekes.blogspot.nl/2013/07/west-eurasian-admixture-in-khoe-san-via.html

bicicleur 2 · Sep 15, 2015

Angela said:
It used to be thought that the Gravettian grew out of the Aurignacian:
http://www.academia.edu/3164654/The...d_I_Human_Migrations_and_the_Changing_Climate

More recent thinking (2007)sees it as a new flow of people, but what I have been able to find is papers that see it as an outgrowth of the Ahmarian culture of the eastern Mediterranean. Interestingly, the area on the maps corresponds to the Levant, southern Anatolia.
http://paleo.revues.org/607

If someone has a site for a paper positing an origin in the Caucasus and thus a migration flow from north of it and then west into Europe I'd love to see it.

Hoffecker & Holliday see an origin in Transcaucasia (Georgia) , and further devellopement in Mezmayskaya cave.
Sungir near Moscow would be one of the first gravettian sites in Europe (35 ka). This location is much more north than were Aurignacians went.

https://instaar.colorado.edu/upload...2013-landscape-archaeology-eastern-europe.pdf

They see a link with Ahmarian, but they on that subject they were refuted by Bar-Yosef who says 'there was no Ahmarian or link with it outside the Levant'.
(I don't find the link to Bar-Yosef)

In the paper Hoffecker & Holliday claim that while Aurignacian has left archeological traces in caves and prime locations, Gravettians were much more mobile and roaming the plains where there are no landmarks and it is much more dificult to find the archeological traces left by the Gravettians.

Little is known about Ahmarian.

http://www.aggsbach.de/2010/07/early-upper-paleolithic-at-kebara-cave-israel-2/

Tomenable · Sep 16, 2015

Angela said:
The problematic lineage is "H", given those somewhat controversial Mesolithic "H" samples in Iberia

What is controversial about them?

They were there at low frequency, and those were probably different subclades than those expanding later in Neolithic.

bicicleur said:
I crossed the Caucasus and stayed in Mezmayskaya cave, from where it expanded into Europe 33 ka, they were the Gravettians
the crucial thing was at Mezmayskaya they had developped borers to drill eyes in bone needles
the Gravettians had better clothing and tents and so they outcompeted Aurignacians on the cold steppe which was all over Europe
Aurignacians even didn't know needles

Are you sure? I have googled "Aurignacian needles" and found some results:

"Stone tools from the Aurignacian culture are known as Mode 4, characterised by blades (rather than flakes, typical of mode 2 Acheulean and mode 3 Mousterian) from prepared cores. Also seen throughout the upper paleolithic is a greater degree of tool standardisation and the use of bone and antler for tools such as needles and harpoons."

http://en.wikipedia.org/wiki/Aurignacian#Tools

"In the Czech Republic the archaeological site od Dolni Věstonice, nearly 30,000 years old (...) at the same site delicate bone needles with eyes were found that announce the advent of tailored clothing. A less elegant but still functional needle found in Slovenia dates from the very beginning of the Aurignacian, maybe 10,000 years earlier."

https://books.google.pl/books?id=Ze...snum=2#v=onepage&q=aurignacian needle&f=false

"A coarse form of eyed needle was found at Sergeac in deposits of Middle Aurignacian date by M.Didon"

https://books.google.pl/books?id=4L...z5yVCw&sa=X&oi=book_result&ct=result&resnum=3

epoch · Sep 16, 2015

Angela said:
It used to be thought that the Gravettian grew out of the Aurignacian:
http://www.academia.edu/3164654/The...d_I_Human_Migrations_and_the_Changing_Climate

More recent thinking (2007)sees it as a new flow of people, but what I have been able to find is papers that see it as an outgrowth of the Ahmarian culture of the eastern Mediterranean. Interestingly, the area on the maps corresponds to the Levant, southern Anatolia.
http://paleo.revues.org/607

If someone has a site for a paper positing an origin in the Caucasus and thus a migration flow from north of it and then west into Europe I'd love to see it.

I am just looking at the D-stats of the Oase 1 paper. Firstly, it clearly looks like Oase 1 (one of the first European AMHs) didn't leave anything noticeable in the European population. It is equally distant to Loschbour and East-Asians, for that matter. It seems only very slightly leaning towards MA1 and American Indians. Z value lower than 2. That equidistance to old Europeans and East-Asians seems similar to Ust'ishim. But Ust'Ishims D-stat show it be far more related to about anything other than Oase 1, which points IMO to Oase 1 being an isolate, a dead end.

But look at the affinity of Kostenki 14 to Loschbour! Also, to a lesser extent but still substantial, to MA1.

"We compute D(Non-African[SUB]1[/SUB], Non-African[SUB]2[/SUB]; Early Modern Human, African), to test whether an early modern human (Oase 1, Ust’-Ishim or Kostenki 14) shares more alleles with Non-African[SUB]1[/SUB] (in which case the statistic is positive) or Non-African[SUB]2[/SUB] (negative)."

http://www.nature.com/nature/journal/v524/n7564/fig_tab/nature14558_ST1.html

bicicleur 2 · Sep 16, 2015

Tomenable said:
Are you sure? I have googled "Aurignacian needles" and found some results:

"Stone tools from the Aurignacian culture are known as Mode 4, characterised by blades (rather than flakes, typical of mode 2 Acheulean and mode 3 Mousterian) from prepared cores. Also seen throughout the upper paleolithic is a greater degree of tool standardisation and the use of bone and antler for tools such as needles and harpoons."

http://en.wikipedia.org/wiki/Aurignacian#Tools

"In the Czech Republic the archaeological site od Dolni Věstonice, nearly 30,000 years old (...) at the same site delicate bone needles with eyes were found that announce the advent of tailored clothing. A less elegant but still functional needle found in Slovenia dates from the very beginning of the Aurignacian, maybe 10,000 years earlier."

https://books.google.pl/books?id=Ze...snum=2#v=onepage&q=aurignacian needle&f=false

"A coarse form of eyed needle was found at Sergeac in deposits of Middle Aurignacian date by M.Didon"

https://books.google.pl/books?id=4L...z5yVCw&sa=X&oi=book_result&ct=result&resnum=3

I must admit I'm a bit surprised.
Aurgnacians had bone tools and flutes indeed, but needles?
If Aurignacians had needles at all, then certainly much less than Gravettian.
I'm not sure the Dolni Vestonice is Aurignacian, it might be Gravettian
And otherwise they talk about 'a coarse form'
There were many needles with Gravettian, and in paleolithic Siberia too, but not in Aurignacian
At first the eyes in the needles were polished, which required a lot of work.
+/- 36 ka in Mezmayskaya Cave the first eyes were drilled in the needles.

the 13000 drilled beads of the Sungir man demonstrates the drilling skills.

https://en.wikipedia.org/wiki/Sungir

Teasers: Anatolians of 6300 BC Y DNA G2a, ancestral to EEF

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