6.5 ka Levantine chalcolithic DNA

[Ygorcs]

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.

[Angela]

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.

[davef]

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

[Ygorcs]

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.

[bicicleur]

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/1474072/1...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.

[bicicleur]

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.

are you sure about the blue eyes in Anatolia?
which part? Central Anatolia or the northwest?

[bicicleur]

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.

well, there is also this :

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.

[davef]

are you sure about the blue eyes in Anatolia?
which part? Central Anatolia or the northwest?

I wouldn't be surprised. Anatolian farmers had whg ancestry, which gave them blue eyes I guess

[Angela]

are you sure about the blue eyes in Anatolia?
which part? Central Anatolia or the northwest?

Yes, I'm sure.

This section on pigmentation is from Hofmanova et al. It's a very good review showing all the instances known up to that time for lighter pigmentation alleles in ancient.

Hofmanova found only one blue-eyed sample in Anatolia. It was from Barcin.

See:
http://journals.plos.org/plosbiology...o.2003703.s013


"Light eye pigmentation variants were present at high frequencies in WHG, SHG, EHG and EEF (notpresent in PEHG), while the blue-eye color founder haplotype h-1 was found in the La Brana,Loschbour, Villabruna WHGs, SF12, Motala1 and Motala12 SHGs and at least one early farmer. Suchresults suggest that the blue eye-color allele is rather old. Using an ABC modeling approach Nakagomeet al. [31], predicted that the light-pigmentation allele at rs12913832 emerged around 42,000 years agoor earlier; a date close in time to the initial peopling of Europe. A plausible scenario of the origin of theblue-eye mutation that reconciles our results with findings from other studies is one where this variantappeared in an ancestral population before the ancestors of the WHG migrated from Near East intoWest and Central Europe [1]."

Then there's Mathiesen et al. 2015.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4918750/

The summary is in Figure 3, but there's a lot more detail if you read it.

[bicicleur]

Yes, I'm sure.

This section on pigmentation is from Hofmanova et al. It's a very good review showing all the instances known up to that time for lighter pigmentation alleles in ancient.

Hofmanova found only one blue-eyed sample in Anatolia. It was from Barcin.

See:
http://journals.plos.org/plosbiology...o.2003703.s013


"Light eye pigmentation variants were present at high frequencies in WHG, SHG, EHG and EEF (notpresent in PEHG), while the blue-eye color founder haplotype h-1 was found in the La Brana,Loschbour, Villabruna WHGs, SF12, Motala1 and Motala12 SHGs and at least one early farmer. Suchresults suggest that the blue eye-color allele is rather old. Using an ABC modeling approach Nakagomeet al. [31], predicted that the light-pigmentation allele at rs12913832 emerged around 42,000 years agoor earlier; a date close in time to the initial peopling of Europe. A plausible scenario of the origin of theblue-eye mutation that reconciles our results with findings from other studies is one where this variantappeared in an ancestral population before the ancestors of the WHG migrated from Near East intoWest and Central Europe [1]."

Then there's Mathiesen et al. 2015.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4918750/

The summary is in Figure 3, but there's a lot more detail if you read it.

yes, but Barcin is northwest-Anatolia, not central Anatolia
among the 8.4 ka Barcin samples there were also I2 (I2c)
as a matter of facts, I2 is suspected to have expanded from SE Europe or maybe even Anatolia around 15 ka, spreading the blue eyes into mesolithic western Europe

but indeed, I2 need not be the unique source for blue eyes, as the paper claims the allele would be 42.000 yo

[Angela]

yes, but Barcin is northwest-Anatolia, not central Anatolia
among the 8.4 ka Barcin samples there were also I2 (I2c)
as a matter of facts, I2 is suspected to have expanded from SE Europe or maybe even Anatolia around 15 ka, spreading the blue eyes into mesolithic western Europe

but indeed, I2 need not be the unique source for blue eyes, as the paper claims the allele would be 42.000 yo

Never said where it was, nor do I think it's particularly relevant. I'm rather persuaded by Hofmanova that it originated in what is now the Near East, as another paper also found, and then moved to Europe with WHG/UHG. Founder effect in a very small population probably took care of the rest.

If it wasn't around Anatolia somewhere, then somewhere in southeastern Europe I would think, as the Reich Lab have been hinting for a long time (i.e. one or the other). Plenty of time in all those thousands of years for it to move around, although it doesn't seem as if it reached the Zagros until later on.

Interestingly it wasn't just the case that the Barcin sample carried the alleles, but like the WHG and SHG it carried the founder haplotype. It would have been interesting to know what the case was for the rest of the Anatolia Neolithic samples, i.e. the ones in the Mathiesen et al paper.

[Salento]

Salento:
She’s Italian like me. STOP IT.
Don’t ruin all this Threads.

Thank you Salento. I appreciate it.

Sorry for the confusion.

[Vallicanus]

She’s Italian like me. STOP IT.
Don’t ruin all this Threads.

Croatthing isn't white, he's a Balkan melange.

[bicicleur]

Never said where it was, nor do I think it's particularly relevant. I'm rather persuaded by Hofmanova that it originated in what is now the Near East, as another paper also found, and then moved to Europe with WHG/UHG. Founder effect in a very small population probably took care of the rest.
If it wasn't around Anatolia somewhere, then somewhere in southeastern Europe I would think, as the Reich Lab have been hinting for a long time (i.e. one or the other). Plenty of time in all those thousands of years for it to move around, although it doesn't seem as if it reached the Zagros until later on.
Interestingly it wasn't just the case that the Barcin sample carried the alleles, but like the WHG and SHG it carried the founder haplotype. It would have been interesting to know what the case was for the rest of the Anatolia Neolithic samples, i.e. the ones in the Mathiesen et al paper.

no, you didn't say, but I asked
and I asked because I believe it could be relevant
because in NW the connection with I2 is much more likely than in Central Anatolia

[Wonomyro]

Croatthing isn't white, he's a Balkan melange.

You are not much differrent from him in some matters. Are you?

[halfalp]

Nonetheless, if those samples are of so much good quality and that they show genes for Blue Eyes, then the mutation appear in an ancestral population that have given ancestors to WHG, Anatolian_Nhl ( probably Anatolian Hunter Gatherers too ), and as far as the Near-East and maybe Iran. Like redhairs, it probably was already common in the finale paleolithic ( some Iberomaursian sample shows 1 or 2 genes for redhairs ) and some related population but not fixed, and over the years those related tribes expanded in west-eurasia in different tribes that have a common ancestor related to those tribes. We might never found the good pop, but transitionnal population, for exemple Paleolithic / Neolithic Anatolia could have been a transitional zone were Blue Eyes expanded without being from there originally, we might only found at some point a population ( i guess after the Neolithic ) that have multiple case of those features and that we can conclude ( this population have so much Blue Eyes genes in various individuals, that they certainly participate to his modern prevalence ).

[bicicleur]

I2 was formed 27.5 ka, TMRCA 21.8 ka
but I2 was probably centered somewhere in a small area in SE Europe or Anatolia till the Villabruna expansion some 15 ka

question is did blue eyes originate in I2 or did it earlier?
and if so, when and where?

if I understand well, these Peqi'in did not only have blue eyes, but also pale skin, which I2 didn't have
but both were probably present in the EEF/WHG contact zone

[Angela]

I2 was formed 27.5 ka, TMRCA 21.8 ka
but I2 was probably centered somewhere in a small area in SE Europe or Anatolia till the Villabruna expansion some 15 ka

question is did blue eyes originate in I2 or did it earlier?
and if so, when and where?

if I understand well, these Peqi'in did not only have blue eyes, but also pale skin, which I2 didn't have
but both were probably present in the EEF/WHG contact zone

Yes, I think that's right. It may just boil down to what alleles happened to be present in the founding population in Europe.

[Sile]

Nonetheless, if those samples are of so much good quality and that they show genes for Blue Eyes, then the mutation appear in an ancestral population that have given ancestors to WHG, Anatolian_Nhl ( probably Anatolian Hunter Gatherers too ), and as far as the Near-East and maybe Iran. Like redhairs, it probably was already common in the finale paleolithic ( some Iberomaursian sample shows 1 or 2 genes for redhairs ) and some related population but not fixed, and over the years those related tribes expanded in west-eurasia in different tribes that have a common ancestor related to those tribes. We might never found the good pop, but transitionnal population, for exemple Paleolithic / Neolithic Anatolia could have been a transitional zone were Blue Eyes expanded without being from there originally, we might only found at some point a population ( i guess after the Neolithic ) that have multiple case of those features and that we can conclude ( this population have so much Blue Eyes genes in various individuals, that they certainly participate to his modern prevalence ).

Other papers also state that the blue eyes did not come from Ukraine/Russian areas

[bicicleur]

Yes, I think that's right. It may just boil down to what alleles happened to be present in the founding population in Europe.

I believe that I2 had contact with the proto-Anatolian G2a 15 ka prior to the Villabruna expansion, somewhere around the Aegean Sea (maybe the Franchthi Cave). They learned about geometric microliths and the bow and arrow prior to their expansion, which wllready existed in the Levant (Kebaran) and in the Zagros Mts (Zarzian). Though their was an exchange in knowledge, DNA excahnge remained rather limited.

The Hamburg culture reindeer hunters (17.5-15.1 ka) were Magdalenian derived (El Miron cluster people), they hunted with the atlatl and had epigravettian-like tools. https://en.wikipedia.org/wiki/Hamburg_culture
They were replaced by the Ahrensburg reindeer hunters (14.9-13.7 ka) with bow and arrow. They were Villabruna cluster people. https://en.wikipedia.org/wiki/Ahrens...ture#Stellmoor


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

Obsidian from the island of Melos appears at Franchthi as early as 13,000 BCE, offering the earliest evidence of seafaring and navigational skills by anatomically modern humans in Greece.[10]

that was 15 ka, and not only obsidian arrived there, also seeds from Anatolia

[bicicleur]

the Hensbacka group were successors of the Ahrensburg reindeer hunters who became seal hunters and fishers and moved up north along the fjords of Norway reaching the North Cape
https://en.wikipedia.org/wiki/Ahrens...ensbacka_group
in North Cape they mixed with EHG from Karelia, this mixture formed the SHG
they were I2, but not darkhaired and darkskinned any more, they were blond and pale skinned,
but back in southern Scandinavia and northern Poland their DNA got diluted with more darkhaired and darkskinned WHG
their story is told in the Günther 2017 paper : http://journals.plos.org/plosbiology...l.pbio.2003703

[O Neill]

So this 50% at 7 ka, In the levent seems to have dropped to 0% after about 3 ka.
Is that correct ? Would you expect then that we might find Similar for greece and turkey ?

That's troy in turkey dead and buried then, the story was imported to greece from somewhere were blonde people still lived in 1200 bc.

[bicicleur]

So this 50% at 7 ka, In the levent seems to have dropped to 0% after about 3 ka.
Is that correct ? Would you expect then that we might find Similar for greece and turkey ?

That's troy in turkey dead and buried then, the story was imported to greece from somewhere were blonde people still lived in 1200 bc.

blond hair in SHG may have died out, but there were other areas where blond hair existed

one of them is the EHG area

and I'm not sure, but wasn't there some blond hair in the Mal'ta and Afantova Gora area?
they didn't take it along to America, for sure

[halfalp]

blond hair in SHG may have died out, but there were other areas where blond hair existed

one of them is the EHG area

and I'm not sure, but wasn't there some blond hair in the Mal'ta and Afantova Gora area?
they didn't take it along to America, for sure

I think AG 2 or 3 had some genes for Blonde Hairs.

[halfalp]

Other papers also state that the blue eyes did not come from Ukraine/Russian areas

We probably never know from where they came. Cheddar Man had Blue Eyes and Levantine Chalcolithic too, they probably have a common denominator, so we can roughly say that Blue Eyes emerged in Western Eurasia.