6.5 ka Levantine chalcolithic DNA

Because it's not to others, especially people who dont have blue eyes ( wich i'am part of ) to call people with blue eyes out like they are shit. Racial bias and sexual bias are real things, wich i personnally dont care about, but a lot of people want to deconstruct those things. It's bad if you are a white guy having sexual bias over blonde blue eyed girl, but it's not if having over an african or a racial minority. It should be pretty obvious that fair features doesn't gives you any power, i dont understand your comment against racism here. So you cannot considering somebody special if he as blue eyes and blonde hair? its against every people that doesn't have those features? It's sad that such targeted shaming is happenning to Europe. And finally, what the heck have indo-european cultures to do with all this crap? Do you see warriors around you? Is Sweden a pride viking country? If you know actuality, then you know thats not. What IE was 4000 years ago, is not what it is today, this is for this reason i believe things like nationalism are bullshit, because those are federative ideas, you are willing to believe that everyone from your ethnic thinks the same, if it was the case, there would not be any other humans than europeans in europe.

Dude, you're a bit obsessed about this. It's no shaming and no attack (like they are shit, what?) to say that blue-eyed people may not have inherited these traits from Eastern European steppe peoples, and that Middle Eastern populations may have had some contribution in the spread of that traits. Unless, of course, you think that there is something especially superior about Eastern Europe or steppe Indo-Europeans, and simultaneously something really shameful and. No self-aware blue-eyed person would feel offended by the mere suggestion (even if it end up being totally wrong) that the high frequencies of blue eyes in their nations may be a relatively recent situation and that blue eyes may have already existed in high frequency in parts of the Middle East before it achieved high frequency in the Pontic-Caspian steppe. Most blue-eyed people won't even know what the Pontic-Caspian steppe is, to be honest.

No, I don't think there's anything "special" about someone having blue eyes or blonde hair - not brown hair, red hair. It may be interesting, beautiful, exotic, fascinating, rare in some regions, but why woud some human being be "special" or "better" because of that? That statement is not just naive, but it's also problematic if you don't choose to ignore the very ugly and dangerous history of racism and white supremacism (particularly of the kind obsessed with "North European looks" - blonde, blue-eyed, very pale) in the very recent past, just decades ago. Statements have a history and a context that either justifies it or makes it even worse. You can't ignore historic and social context. Black pride usually means, in practice, something very different in society than white/blue eyes pride, let alone an even stronger assertion which is people with blue eyes are "special".
 
Well, but if some people in 2018 still believe that PIE people were all Nordic types with blonde hair and blue eyes then I can see why a geneticist may have thought it'd be nice (or funny?) to call them out ("attack" is too strong a word frankly). I don't think the point of this comparison has two interesting observations: 1) things can change a lot in 5,000-6,000 years, so that the frequency of blue eyes in the Levant and in Eastern Europe are now almost the reverse of what they were in ~4000 BCE; 2) the traditional anthropologists and the pseudo-scientific or simply amateur/deluded racists of older generations were indeed very wrong when they believed that blue eyes and blonde hair were directly and mostly correlated with Indo-European ancestry, because there were other clearly non-IE sources for those traits. Unless blue eyes, light skin and blonde hair are somehow "more special" if they came only from Eastern Europe rather than at least partly from West Asia and from Western/Central Europe itself, I don't get what's the "big problem" in that provocation. The racists were again dead wrong. I can see why someone would find it worth commenting about.

I think the hypothesis was more than just a racist fantasy, since modern frequencies of light pigmentation correlate very well with the extent of Corded Ware culture. Coon was very careful in his wording when he described that skeletally the steppe people were of a type that today is associated with blue eyes & blondism. He cites notable exceptions to this in Iran, East Africa etc. .
 
I feel like, in linguistic afro-asiatic hypothesis are too conservative to try to debunk the actual hypothesis with some genetic facts. What's actually the real relationship between Afro-Asiatic languages? Some people have actual problem to consider even IE languages family as a thing, so imagine A/A?

It's only suppositions here, concerning AA. Concerning reality of IE, I think sincerely things are clear enough and well shored;
 
with some fancy we could suppose the definite break of Semitic off other AA languages could have occurred when somme AA language came northwards and was adopted by more northern populations in ancient times, if I follow your suggestion or what I believe it is. After that, linguistically acculturated northern pops could have reversed the flood and passed a completely developped Semitic language to southern pops, their old "teachers" of more archaic AA... Not impossible at all. Latins were not the first basic IE speakers but after some time, when their culture and forces flourished they passed their locally evolved IE to other IE pops whose languages were maybe closer to the origins...

That's a very possible scenario. My personal hunch though is that there was a confluence in the region between the "highland West Asia" and the "lowland West Asia" (northern Syria & Iraq - southern Turkey), during the Neolithic, between Iranian_Neolithic, Anatolian_Neolithic and Levant_Neolithic (speaking an earlier Afro-Asiatic branch out of which Proto-Semitic eventually arose, much like Latin from an earlier Northwestern IE that was mostly absorbed by it in a large territory). The Levant_Neolithic was possibly there first and was initially dominant during the Neolithic, absorbing the "northern" elements around its territory, until these northern elements, as you say, reversed the flood and started to expand onto the Levant_Neolithic and became dominant by the Chalcolithic, consolidating this mixed Proto-Semitic population. Then this heavily Iranian/Anatolian-shifted, very changed "Levant_Neolithic" population descended to the rest of "lowland West Asia" during the Late Chalcolithic or right after the Chalcolithic.
 
Dude, you're a bit obsessed about this. It's no shaming and no attack (like they are shit, what?) to say that blue-eyed people may not have inherited these traits from Eastern European steppe peoples, and that Middle Eastern populations may have had some contribution in the spread of that traits. Unless, of course, you think that there is something especially superior about Eastern Europe or steppe Indo-Europeans, and simultaneously something really shameful and. No self-aware blue-eyed person would feel offended by the mere suggestion (even if it end up being totally wrong) that the high frequencies of blue eyes in their nations may be a relatively recent situation and that blue eyes may have already existed in high frequency in parts of the Middle East before it achieved high frequency in the Pontic-Caspian steppe. Most blue-eyed people won't even know what the Pontic-Caspian steppe is, to be honest.

No, I don't think there's anything "special" about someone having blue eyes or blonde hair - not brown hair, red hair. It may be interesting, beautiful, exotic, fascinating, rare in some regions, but why woud some human being be "special" or "better" because of that? That statement is not just naive, but it's also problematic if you don't choose to ignore the very ugly and dangerous history of racism and white supremacism (particularly of the kind obsessed with "North European looks" - blonde, blue-eyed, very pale) in the very recent past, just decades ago. Statements have a history and a context that either justifies it or makes it even worse. You can't ignore historic and social context. Black pride usually means, in practice, something very different in society than white/blue eyes pride, let alone an even stronger assertion which is people with blue eyes are "special".

I mean, you are probably a little too much obsessed with racism history, because this is actually how humanity is thinking. As i said, people have sexual bias, they could found some physical characteristics special. I dont get the Eastern European / Steppe People superiority because as far as i remember, classic racists despise eastern europe and steppe peoples. The fact that those 6000 years old Levante people isn't even a question in Virtue Signaling europeans because Villabruna and Cheddar Man are 3 times older and had Blue Eyes ( if we want to start talking about facts ).
 
Concerning pigmentation, always the same old thing and oppositions!
But statistically speaking, the ancient samples we have everywhere are very too small as a whole to built solid hypothesis. THese traits are based upon too few SNP's compared to complete auDNA, when a sample of 10 persons in a little region is quite sufficiant for auDNA to have a valuable sketch. For pigmentation we need a far bigger number of persons by region than what we have to date for ancient pops.
 
I mean, you are probably a little too much obsessed with racism history, because this is actually how humanity is thinking. As i said, people have sexual bias, they could found some physical characteristics special. I dont get the Eastern European / Steppe People superiority because as far as i remember, classic racists despise eastern europe and steppe peoples. .

We're talking about supposedly special people, not special physical features. You're getting a bit confused about what we're talking about here. As for "classic racists", they've long been reconciled with the increasing evidence of Indo-Europeans coming from Eastern Europe and just consider that modern Eastern Europeans and steppe peoples would've become inferior due to extensive racial mixing with "inferior peoples", especially East Asians and Central Asians/Middle Easterners (e.g. Turks). They consider them disparagingly mongrels and half-breeds who lost their racial purity supposedly better preserved by Northern Europeans. I think you missed that part, it's everywhere on the internet.
 
I think the hypothesis was more than just a racist fantasy, since modern frequencies of light pigmentation correlate very well with the extent of Corded Ware culture. Coon was very careful in his wording when he described that skeletally the steppe people were of a type that today is associated with blue eyes & blondism. He cites notable exceptions to this in Iran, East Africa etc. .

Yes, but only partially. Those cultures were not PIE and not the original source of Indo-European expansion, though, but just descendants of the PIE-speaking culture(s) already mixed to varying levels with other regional populations. The very light phenotype of CWC or Sintashta people did not exist in near fixation frequencies in earlier cultures that are much more likely to be representative of the original, still undivided PIE. Besides, SHG, GAC and now Chalcolithic Levant and increasingly many other cultures also show that light skin, blue eyes and blonde hair - either cumulatively or only some of those traits - were already widespread in many other regions even before the Indo-European incursions in those areas, so they could've been one among several contributors to the spread of those phenotypic features, but they were certainly not pioneers nor the epicenter of that change.
 
The issue is not that. It is that Chalcolithic Levant was already northern-shifted (much more Anatolian_Neo and, a bit less so, Iranian_Neo) than Neolithic Levant, but this study also shows that Chalcolithic Levant was still less northern-shifted than Bronze Age Levant, particulary Bronze Age Levant_North (that's especially clear when you look at the PCA, with Chalcolithic Levant closer to Neolithic Levant, and Bronze Age Levant, especially Bronze Age Levant North, even closer to the ancient Caucasian and Iranian samples). That shows that, if Chalcolithic Levant can be modeled as ~43% non-Levantine (Anatolian + Iranian), then Bronze Age Levant were even more affected by these West Asia, but non-Levantine sources of ancestry. In my opinion that came from a second wave from northerners, probably this time more influenced by Iranians/South Caucasians than by Anatolians (maybe the wave that brought a huge percentage of J1 and J2?) - and in my opinion probably more "northeasterly" than the earlier wave and possibly coming roughly from Northern Mesopotamia.

Seems like you are avoiding the question.........semitic language began after these people left the levant ( disappeared ) in the early bronze-age .
these people could never have brought semetic to the levant and mixed with the existing populace because semetic had not even begun.
The migrants brought another language with them from NE Anatolia/South caucasus or beyond lands
 
the best of the ancient samples so far............results mean more accurate analysis
The data extracted from the skeletal remains, taken from 22 individuals, “is of exceptional quality given the typically poor preservation of DNA in the warm Near East,” wrote the scientists.
According to Tel Aviv University’s Hershkovitz, “human DNA was preserved in the bones of the buried people in Peki’in cave, likely due to the cool conditions within the cave and the limestone crust that covered the bones and preserved the DNA.”
As a result, the researchers were able to do a whole genome analysis of 22 of the skeletons.
“This study of 22 individuals is one of the largest ancient DNA studies carried out from a single archaeological site, and by far the largest ever reported in the Near East,” said Tel Aviv University researcher May.
The scientists uncovered some recessive genetic traits not usually expected in human remains from the Levant.
 
Seems like you are avoiding the question.........semitic language began after these people left the levant ( disappeared ) in the early bronze-age .
these people could never have brought semetic to the levant and mixed with the existing populace because semetic had not even begun.
The migrants brought another language with them from NE Anatolia/South caucasus or beyond lands

I think you just did not understand my point. Nobody said that Levant_Chalcolithic is necessarily the Proto-Semitic people, but that these findings confirm that the cultural and genetic transformation of the Levant from the Neolithic to the Bronze Age (when it had become clearly Semitic in its vast majority) was marked by northern (Anatolian + Iranian/Caucasian) influx, not by massive south-to-north movements as some proponents of a "southern" Proto-Semitic language had proposed. That's all.

Actually, Proto-Semitic is a Chalcolithic language, it's estimated to have started splitting as early as 3750 BCE (latest common, completely unified stage of the language), so it's reasonable to expect that by 4000 BCE some early form of Proto-Semitic was already in use. By 2400 BCE Semitic daughter languages, Eblaite and a little later Akkadian, were already present at least in Syria and Iraq, possibly also elsewhere further south, and those East Semitic languages had already acquired some characteristics that made them distinct from West & South Semitic languages.

As a matter of fact, Bronze Age_Levant, both Levant_North and Levant_South, are even more northern-shifted than Levant_Chalcolithic and obviously much more than Levant_Neolithic, so what happened from the Chalcolithic to the Bronze Age clearly brought a population that was even more heavy in Chalcolithic Iranian-like admixture... and exactly because of that, that population most probably came from the north(east). And what also happened during that period was the widespread expansion of Proto-Semitic-derived languages.

Also, Levantine Chalcolithic people were clearly ancestral to Bronze Age Semitic population of the Levant (Levant_Bronze Age_North is best modeled as a mixture of Levant_Chalcolithic + Iran_Chalcolithic), and (yet unsampled) parts of the Chalcolithic Levant may have simply missed the Anatolian_Neolithic introgression seen in the Peqi'in Cave remains but also lingered on and contributed to Levant_Bronze Age_South. That's what the scholars of this study concluded themselves.

So you clearly misinterpreted the paper (or maybe didn't read it entirely). The Chalcolithic Levantines did not just vanish, they certainly contributed genetically and culturally to the future of the region, even if they were not the original Proto-Semites, which is actually my point since the beginning, since I think Proto-Semitic arose in Northern Mesopotamia and spread from there during the Late Chalcolithic and Early Bronze Age.

Read:

The presence of Iran_ChL-related ancestry in both populations – but not in the earlier Levant_N – suggests a history of spread into the Levant of peoples related to Iranian agriculturalists, which must have occurred at least by the time of the Chalcolithic. The Anatolian_N component present in the Levant_ChL but not in the Levant_BA_South sample suggests that there was also a separate spread of Anatolian-related people into the region. The Levant_BA_South population may thus represent a remnant of a population that formed after an initial spread of Iran_ChL-related ancestry into the Levant that was not affected by the spread of an Anatolia_N-related population, or perhaps a reintroduction of a population without Anatolia_N-related ancestry to the region.

We observe a qualitatively different pattern in the Levant_BA_North samples from Sidon, Lebanon, where models including Levant_ChL paired with either Iran_N, Iran_LN, or Iran_HotuIIIb populations appear to be a significantly better fit than those including Levant_N + Iran_ChL. We largely confirm this result using the “Right” population outgroups defined in26. (abb. Haber: Ust_Ishim, Kostenki14, MA1, Han, Papuan, Ami, Chuckhi, Karitiana, Mbuti, Switzerland_HG, EHG, WHG, and CHG), although we find that the specific model involving Iran_HotuIIIb no longer works with this “Right” set of populations. Investigating this further, we find that the addition of Anatolia_N in the “Right” outgroup set excludes the model of Levant_N + Iran_ChL favored by26. These results imply that a population that harbored ancestry more closely related to Levant_ChL than to Levant_N contributed to the Levant_BA_North population, even if it did not contribute detectably to the Levant_BA_South population.

The addition of the Levant_ChL causes the model to fail, indicating that Levant_BA_South and Levant_ChL share ancestry following the separation of both of them from the ancestors of Levant_N and Iran_ChL. Thus, in the past there existed an unsampled population that contributed both to Levant_ChL and to Levant_BA_South, even though Levant_ChL cannot be the direct ancestor of Levant_BA_South because, as described above, it harbors Anatolia_N-related ancestry not present in Levant_BA_South.
 
26 % Anatolia N, blue eyes and copper metallurgie
could there be some connection with Vinca?
 
there would have been 2 different succesive chalcolithic cultures in the Levant :

Chalcolithic
(4500 BCE – 3300 BCE)
Early Chalcolithic 4500 BCE – 4000 BCE
Late Chalcolithic (Ghassulian) 4000 BCE – 3300 BCE

So this would have been early chalcolithic, not the Ghassulian.

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

Settlements belonging to the Ghassulian culture have been identified at numerous other sites in what is today southern Israel, especially in the region of Beersheba, where elaborate underground dwellings have been excavated. The Ghassulian culture correlates closely with the Amratian of Egypt and also seems to have affinities (e.g., the distinctive churns, or “bird vases”) with early Minoan culture in Crete.[3][6]
 
I think you just did not understand my point. Nobody said that Levant_Chalcolithic is necessarily the Proto-Semitic people, but that these findings confirm that the cultural and genetic transformation of the Levant from the Neolithic to the Bronze Age (when it had become clearly Semitic in its vast majority) was marked by northern (Anatolian + Iranian/Caucasian) influx, not by massive south-to-north movements as some proponents of a "southern" Proto-Semitic language had proposed. That's all.

Actually, Proto-Semitic is a Chalcolithic language, it's estimated to have started splitting as early as 3750 BCE (latest common, completely unified stage of the language), so it's reasonable to expect that by 4000 BCE some early form of Proto-Semitic was already in use. By 2400 BCE Semitic daughter languages, Eblaite and a little later Akkadian, were already present at least in Syria and Iraq, possibly also elsewhere further south, and those East Semitic languages had already acquired some characteristics that made them distinct from West & South Semitic languages.

As a matter of fact, Bronze Age_Levant, both Levant_North and Levant_South, are even more northern-shifted than Levant_Chalcolithic and obviously much more than Levant_Neolithic, so what happened from the Chalcolithic to the Bronze Age clearly brought a population that was even more heavy in Chalcolithic Iranian-like admixture... and exactly because of that, that population most probably came from the north(east). And what also happened during that period was the widespread expansion of Proto-Semitic-derived languages.

Also, Levantine Chalcolithic people were clearly ancestral to Bronze Age Semitic population of the Levant (Levant_Bronze Age_North is best modeled as a mixture of Levant_Chalcolithic + Iran_Chalcolithic), and (yet unsampled) parts of the Chalcolithic Levant may have simply missed the Anatolian_Neolithic introgression seen in the Peqi'in Cave remains but also lingered on and contributed to Levant_Bronze Age_South. That's what the scholars of this study concluded themselves.

So you clearly misinterpreted the paper (or maybe didn't read it entirely). The Chalcolithic Levantines did not just vanish, they certainly contributed genetically and culturally to the future of the region, even if they were not the original Proto-Semites, which is actually my point since the beginning, since I think Proto-Semitic arose in Northern Mesopotamia and spread from there during the Late Chalcolithic and Early Bronze Age.

Read:

Iran Chalcolithic definitely is part of Bronze Age Levant. However, aren't the authors saying that Levant Chalcolithic did not genetically impact either North or South Bronze Age?

@Bicicleur,
So what is the culture of the early Chalcolithic in the Levant, what is its origin and spread?

Are you aware of any attested archaeological traces from Europe to Anatolia or the Levant from Vinca in the appropriate time frame? Also, there were blue eyes in the Anatolia Neolithic and even one in Levant Neolithic if I remember correctly, so no need for the snps to be reintroduced from Europe.
 
Iran Chalcolithic definitely is part of Bronze Age Levant. However, aren't the authors saying that Levant Chalcolithic did not genetically impact either North or South Bronze Age?

@Bicicleur,
So what is the culture of the early Chalcolithic, what is its origin and spread?

I didn't interpret thist way. For me it is stated that Levant_Chalcolithic probably contributed to Levant_BA_North, but not directly Levant_BA_South.

But about the latter it is possible, according to them, that the Levant_Chalcolithic population of the Peqi'in cave represents a population that received this additional Anatolian_Neolithic wave, but other populations of the Chalcolithic Levant may have went on unaffected by the Anatolian_Neolithic influx, so the Levant_BA_South can plausibly be at least partially the descendant of a Levant Chalcolithic population that resisted the Anatolian_Neolithic introgression and received an additional Iran_Chalcolithic one.

The Anatolian_Neolithic path could have been separated from the Iran_Chalcolithic one, not coming from the very same population/region. I think it's highly likely that the Levant, during this process of genetic interaction between Anatolia, Levant and Iran/Caucasus, had a lot of population substructure until much later, when the homogeneization that ensued was more or less complete (possibly by the Late Bronze Age). See these parts of the study:

The presence of Iran_ChL-related ancestry in both populations – but not in the earlier Levant_N – suggests a history of spread into the Levant of peoples related to Iranian agriculturalists, which must have occurred at least by the time of the Chalcolithic. The Anatolian_N component present in the Levant_ChL but not in the Levant_BA_South sample suggests that there was also a separate spread of Anatolian-related people into the region. The Levant_BA_South population may thus represent a remnant of a population that formed after an initial spread of Iran_ChL-related ancestry into the Levant that was not affected by the spread of an Anatolia_N-related population, or perhaps a reintroduction of a population without Anatolia_N-related ancestry to the region.

We observe a qualitatively different pattern in the Levant_BA_North samples from Sidon, Lebanon, where models including Levant_ChL paired with either Iran_N, Iran_LN, or Iran_HotuIIIb populations appear to be a significantly better fit than those including Levant_N + Iran_ChL. We largely confirm this result using the “Right” population outgroups defined in26. (abb. Haber: Ust_Ishim, Kostenki14, MA1, Han, Papuan, Ami, Chuckhi, Karitiana, Mbuti, Switzerland_HG, EHG, WHG, and CHG), although we find that the specific model involving Iran_HotuIIIb no longer works with this “Right” set of populations. Investigating this further, we find that the addition of Anatolia_N in the “Right” outgroup set excludes the model of Levant_N + Iran_ChL favored by26. These results imply that a population that harbored ancestry more closely related to Levant_ChL than to Levant_N contributed to the Levant_BA_North population, even if it did not contribute detectably to the Levant_BA_South population.


The addition of the Levant_ChL causes the model to fail, indicating that Levant_BA_South and Levant_ChL share ancestry following the separation of both of them from the ancestors of Levant_N and Iran_ChL. Thus, in the past there existed an unsampled population that contributed both to Levant_ChL and to Levant_BA_South, even though Levant_ChL cannot be the direct ancestor of Levant_BA_South because, as described above, it harbors Anatolia_N-related ancestry not present in Levant_BA_South.
 
I didn't interpret thist way. For me it is stated that Levant_Chalcolithic probably contributed to Levant_BA_North, but not directly Levant_BA_South.

But about the latter it is possible, according to them, that the Levant_Chalcolithic population of the Peqi'in cave represents a population that received this additional Anatolian_Neolithic wave, but other populations of the Chalcolithic Levant may have went on unaffected by the Anatolian_Neolithic influx, so the Levant_BA_South can plausibly be at least partially the descendant of a Levant Chalcolithic population that resisted the Anatolian_Neolithic introgression and received an additional Iran_Chalcolithic one.

The Anatolian_Neolithic path could have been separated from the Iran_Chalcolithic one, not coming from the very same population/region. I think it's highly likely that the Levant, during this process of genetic interaction between Anatolia, Levant and Iran/Caucasus, had a lot of population substructure until much later, when the homogeneization that ensued was more or less complete (possibly by the Late Bronze Age). See these parts of the study:

Yes, I see all that. There seems to be a bit of internal inconsistency in the paper.

"It was striking to us that previously published Bronze Age Levantine samples from the sites of 'Ain Ghazal in present-day Jordan (Levant_BA_South) and Sidon in present-day Lebanon (Levant_BA_North) can be modeled as two-way admixtures, without the Anatolia_N contribution that is required to model the Levant_ChL population24,26. This suggests that the Levant_ChL population may not be directly ancestral to these later Bronze Age Levantine populations, because if it were, we would also expect to detect an Anatolia_N component of ancestry."

It makes sense to me that some genetic influence would have remained in certain areas.
 
Wondering if there are any modern Levantine groups that still have Anatolian farmer genes from these people. Strange how they didn't make it to the Sidons
 
Yes, I see all that. There seems to be a bit of internal inconsistency in the paper.

"It was striking to us that previously published Bronze Age Levantine samples from the sites of 'Ain Ghazal in present-day Jordan (Levant_BA_South) and Sidon in present-day Lebanon (Levant_BA_North) can be modeled as two-way admixtures, without the Anatolia_N contribution that is required to model the Levant_ChL population24,26. This suggests that the Levant_ChL population may not be directly ancestral to these later Bronze Age Levantine populations, because if it were, we would also expect to detect an Anatolia_N component of ancestry."

It makes sense to me that some genetic influence would have remained in certain areas.

Wow then it seems they're contradicting themselves. It will probably be pointed out and corrected later. When you see the detailed description of the tests they made, it seems clear that Levant_BA_North is different from Levant_BA_South in two ways: 1) Levant_Chalcolithic is a better fit than Levant_Neolithic; and 2) Levant_BA_North requires 3 admixtures to give the best fit, while Levant_BA_South requires only 2. It looks like they were a bit confused with their own results.

Also, I think we should not assume that the entire Chalcolithic Levant was like these Levant_Chalcolithic Peqi'in samples. They mention in the paper that the samples they analyzed form a very genetically homogeneous population, and the very high frequency (49%) of blue eyes is also in my opinion another indication that we may be dealing with a relatively localized genetic structure with some effects from a founder effect or something like that.

Their results demonstrate that Levant_BA_South probably had an ancestral source that contributed to Levant_Chalcolithic, too, so it's possible that we are still missing another part of the Chalcolithic Levant that was not directly affected by that "Anatolian shift" but was there and contributed to later BA populations in the same region.

P.S.: I guess I found the reason for that apparent inconsistency. The keyword is previously published BA Levantine samples in that part of the study. Further in the paper they explain that those studies had modeled them as a two-way admixture probably because they lacked a more proximate source which is Levant_Chalcolithic, and that hid the Levant_Chalcolithic ancestry in the BA_North sample. Those previous studies did not thus observe the genetic heterogeneity between the South and North of BA Levant. See:

W
e applied qpWave again, replacing Levant_ChL with Levant_BA_North, and found that the minimum number of source populations is only two. However, when we include the Levant_ChL population as an additional outgroup, three source populations are again required. This suggests that in the absence of the data from Levant_ChL there is insufficient statistical leverage to detect Anatolian-related ancestry that is truly present in admixed form in the Levant_BA_North population (data from the Levant_ChL population makes it possible to detect this ancestry). This may explain why26 did not detect the Anatolian Neolithic-related admixture in Levant_BA_North.
 
Iran Chalcolithic definitely is part of Bronze Age Levant. However, aren't the authors saying that Levant Chalcolithic did not genetically impact either North or South Bronze Age?

@Bicicleur,
So what is the culture of the early Chalcolithic in the Levant, what is its origin and spread?

Are you aware of any attested archaeological traces from Europe to Anatolia or the Levant from Vinca in the appropriate time frame? Also, there were blue eyes in the Anatolia Neolithic and even one in Levant Neolithic if I remember correctly, so no need for the snps to be reintroduced from Europe.

I didn't say that these people in Israel came from Vinca.
I said there seem to be some things in common.
Maybe these people and Vinca have some common ancestor.
Maybe coming from Catal Höyük or thereabout.

http://discovery.ucl.ac.uk/1474072/...per a review and new work plus Appendices.pdf

No proof of copper melting though, just very early smithing of native copper, which was to be found in Anatolia.
First copper smelting is 7.5 ka in Vinca and Zagros chalcolithic similtaneously. 2 areas very far apart.

We don't have Catal Höyük DNA, but we have Boncüklü and Tepecik-Ciftlik.
Anatolia Neolitic originated in this area.
 

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