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Genetic study Out-of-Anatolia: cultural and genetic interactions during the Neolithic expansion in the Aegean

Omino

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"Abstract
Western Anatolia has been a crucial yet elusive element in the Neolithic expansion from the
Fertile Crescent to Europe. Using 30 new palaeogenomes from Anatolia c.8000-6000 BCE
we describe the early Holocene genetic landscape of Western Anatolia, which reveals
population continuity since the late Upper Pleistocene. Our findings indicate that the
Neolithisation of Western Anatolia in the 7th millennium BCE was a multifaceted process,
characterised by the assimilation of Neolithic practices by indigenous groups and the influx
of populations from the east, their admixed descendants eventually laying the foundations of
Neolithic Southeast Europe. Intriguingly, the observed diversity in material culture among
Aegean Early Neolithic communities correlates with their geographical distances but not their
genetic differences, signifying a decoupling between cultural developments and genetic
admixture processes."

"Conclusion
Our expanded genomic dataset has helped resolve long-standing questions on the earliest
westward steps of the Neolithic expansion beyond the Fertile Crescent. We first describe the
indigenous gene pool of W Anatolia prior to Neolithisation, represented by the 7800 BCE
Girmeler genome, which was closely related to C Anatolians from the PPN period but distinct
in its lack of U Mesopotamian ancestry. The presence of PPN-related cultural elements in
Girmeler provides another case of cultural interaction among regional communities without
major genetic admixture. The fact that we find U Mesopotamia-related admixture during the
PPN in C Anatolia but not in Girmeler is also interesting, raising the possibility that eastern gene flow into C Anatolia >8k BCE may have involved the introduction of certain Neolithic
elements such as mudbrick technology or animal management practices, which either did
not reach Girmeler or were simply not adopted there.

Moving forward in time, we use the Neolithic Aktopraklık genome from c.6600 BCE (Marchi
et al. 2020) to infer that the Pınarbaşı/Girmeler-related indigenous foragers persisted in W
Anatolia at least between c.13ky-6.6ky BCE. We further infer that Neolithisation in the region
involved both large-scale mobility from C Anatolia and cultural adoption by local groups, as
well as admixture between the two. The patterns we observe resemble those observed in N
Africa (Simões et al., 2023), where the expansion of Neolithic communities appears to have
triggered cultural change among locals. Through comparative analysis of material culture
traits and ancient genomes for the first time to our knowledge, we test the hypothesis that
the observed cultural heterogeneity in regions of Neolithic expansion can be explained by
heterogeneity in admixture patterns, but find no support for this. Instead, sociocultural affinity
patterns, even in ritual elements such as burial practices (Figure S35), may have been more
fluid than genetic admixture processes, at least during the Aegean Neolithisation.
Our results raise new questions. One is the sources of gene flow into W Anatolia before
7000 BCE. A second question is the reason for the apparent lack of indigenous genetic
contribution in the Neolithic populations of Greece, which appears unusual given what is
observed in the rest of Europe. Another question pertains to the lack of correlations between
sociocultural and population genetic similarities at the local level: how universal is this
conclusion, and at what levels and historical depth do mobility and admixture cease to shape
cultural affinities? Or may correlations become visible only with more refined classifications
of material culture assemblages and more comprehensive genetic data? Through further
integration of material culture and palaeogenomic data, we are thus starting to disentangle
the diverse sources of cultural shifts in prehistoric societies."

 
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Interesting, it confirms the Neolithic expansion from Anatolia to the Aegean on the Neolithic.
Regarding y Haplogroups:
2 H (H2;H1b1)
1 C (C1a2)
2 J2 (J2a;J2a1)
4 G2 (G2a2a1a;G2a2a1;G2a2b2a1;G2a2b)

In the case of HG J2, maybe it could be J2-L25 or its subclade J2-Z438 (well expanded today in Anatolia and the Aegean islands), demonstrating early movements from the Zagros mountains to the Anatolian Peninsula. This J2 could be related to the DYS445=6 with DYS 391=9 or DYS 391=10, hypothesized as an Anatolian neolithic mark, according to some authors.
 
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Interesting, it confirms the Neolithic expansion from Anatolia to the Aegean on the Neolithic.
Regarding y Haplogroups:
2 H (H2;H1b1)
1 C (C1a2)
2 J2 (J2a;J2a1)
4 G2 (G2a2a1a;G2a2a1;G2a2b2a1;G2a2b)

In the case of HG J2, maybe it could be J2-L25 or its subclade J2-Z438 (well expanded today in Anatolia and the Aegean islands), demonstrating early movements from the Zagros mountains to the Anatolian Peninsula. This J2 could be related to the DYS445=6 with DYS 391=9 or DYS 391=10, hypothesized as an Anatolian neolithic mark, according to some authors.

Where did you see the haplogroups in the paper? Regarding H1b1, that sounds like mtDNA to me. Only the Y-DNA haplogroup H2 has been found as a minor line among neolithic farmers in Anatolia and Europe.
 

Arguments have long suggested that the advent of early farming in the Near East and80
Anatolia was linked to a 'Mother Goddess' cult. However, evidence for a dominant female81
role in these societies has been scarce. We studied social organisation, mobility patterns82
and gendered practices in Neolithic Southwest Asia using 131 paleogenomes from83
Çatalhöyük East Mound (7100-5950 BCE),

1719702666004.jpeg
 
Thank you. This paper interprets ANFs to be a mix of Balkan HGs and Levant_N. That's not making sense. Levant_N itself is a mix of Natufian-related populations and Anatolians.

I agree. ANFs lack Taforalt related ancestry which is part of what makes Natufians and Levant PPN populations distinct from Anatolian HGs and ANFs. The authors' conclusions here are dubious. I also disagree with the author's idea that ANFs are a two way admixture between Mesopotamian N and Pinarbasi HG. I think it's more likely they are a two way admixture between Pinarbasi HG and Caucasian HG groups, with the vast majority of their ancestry being locally derived from Pinarbasi like populations.

Back to the topic of the Levant, it's clear that ANF was supplementing Natufian/Levant PPNA like ancestry and not the inverse. For the Levant, the Iberomarusian contribution we see with Natufians simply decreases as time goes on which indicates a continued reduction in local ancestry in favor of Anatolian, Caucasian, Mesopotamian and possibly Iranian elements.
 
I agree. ANFs lack Taforalt related ancestry which is part of what makes Natufians and Levant PPN populations distinct from Anatolian HGs and ANFs. The authors' conclusions here are dubious. I also disagree with the author's idea that ANFs are a two way admixture between Mesopotamian N and Pinarbasi HG. I think it's more likely they are a two way admixture between Pinarbasi HG and Caucasian HG groups, with the vast majority of their ancestry being locally derived from Pinarbasi like populations.

Back to the topic of the Levant, it's clear that ANF was supplementing Natufian/Levant PPNA like ancestry and not the inverse. For the Levant, the Iberomarusian contribution we see with Natufians simply decreases as time goes on which indicates a continued reduction in local ancestry in favor of Anatolian, Caucasian, Mesopotamian and possibly Iranian elements.
Exactly. It was the other way round. Besides, it has been known since 2019/2020 that ANF derived their ancestry from local hunter-gatherers and that they developed agriculture in situ. They were not a mix of anything but there seems to be an agreement that there was a combined admixture in the range of 10-15% from Caucasus- and Levantine-related sources, maybe even less. And where that admixture is found depends on the geography.

ANF were remarkably expansive. No other ancient West Eurasian population left such a large genetic imprint, the cause of this being a major population explosion due to a highly developed agriculture that could sustain large populations. But space is a limited resource under such circumstances. ANF excursion into the Middle East wasn't nearly as big as into Europe but it still seems that their descendants gave the impetus to the developtment of civilisation in the Middle East. They weren't the only ones, the other influence coming from the Caucasus and present-day Iran. Even though the Natufians are said to have been the first sedentary hunter-gatherers that began to cultivate cereals, they (or populations derived from them) were overrun by the culturally more advanced Anatolians, Caucasians and Iranians. What is remarkable though, is that these invaders were linguistically assimilated. Afroasiatic and its Semitic offshoot is said to come from Natufian-related sources. The later spread of Semitic into Mesopotamia is also fascinating. The oldest toponomy of Syria and Iraq for example is clearly non-Semitic and I'm not only talking about the Sumerians. And here we have another case of adoption of a non-Semitic civilisation by Semitic-speaking peoples. The Babylonians and Assyrians were cultural imitations of the Sumerians, yet the language of the latter was completely replaced.

Why do Levantines tend to be more light-skinned than people of the Arabian peninsula where Natufian-related ancestry reaches its modern peak? Clearly because of the significantly higher Anatolian and Caucasian admixture. All this doesn't mean that there was no increase in Natufian/Levantine admixture in Anatolia but this is the result of later movements, starting mostly with the Bronze Age.

Papers like these raise the question of how many amateurs work in these fields. I say this because I read another dubious paper recently, published by scientists from Sarajevo about medieval mtDNA in Bosnia. Their conclusion: it overlaps mostly with Italy. The haplogroup mutations are more than 2000 years old and can be found all over Europe. Some people may be excellent at collecting samples and sequencing genomes but they seem utterly incompetent at analysing data and drawing the correct conclusions.
 
Exactly. It was the other way round. Besides, it has been known since 2019/2020 that ANF derived their ancestry from local hunter-gatherers and that they developed agriculture in situ. They were not a mix of anything but there seems to be an agreement that there was a combined admixture in the range of 10-15% from Caucasus- and Levantine-related sources, maybe even less. And where that admixture is found depends on the geography.

ANF were remarkably expansive. No other ancient West Eurasian population left such a large genetic imprint, the cause of this being a major population explosion due to a highly developed agriculture that could sustain large populations. But space is a limited resource under such circumstances. ANF excursion into the Middle East wasn't nearly as big as into Europe but it still seems that their descendants gave the impetus to the developtment of civilisation in the Middle East. They weren't the only ones, the other influence coming from the Caucasus and present-day Iran. Even though the Natufians are said to have been the first sedentary hunter-gatherers that began to cultivate cereals, they (or populations derived from them) were overrun by the culturally more advanced Anatolians, Caucasians and Iranians. What is remarkable though, is that these invaders were linguistically assimilated. Afroasiatic and its Semitic offshoot is said to come from Natufian-related sources. The later spread of Semitic into Mesopotamia is also fascinating. The oldest toponomy of Syria and Iraq for example is clearly non-Semitic and I'm not only talking about the Sumerians. And here we have another case of adoption of a non-Semitic civilisation by Semitic-speaking peoples. The Babylonians and Assyrians were cultural imitations of the Sumerians, yet the language of the latter was completely replaced.

Why do Levantines tend to be more light-skinned than people of the Arabian peninsula where Natufian-related ancestry reaches its modern peak? Clearly because of the significantly higher Anatolian and Caucasian admixture. All this doesn't mean that there was no increase in Natufian/Levantine admixture in Anatolia but this is the result of later movements, starting mostly with the Bronze Age.

Papers like these raise the question of how many amateurs work in these fields. I say this because I read another dubious paper recently, published by scientists from Sarajevo about medieval mtDNA in Bosnia. Their conclusion: it overlaps mostly with Italy. The haplogroup mutations are more than 2000 years old and can be found all over Europe. Some people may be excellent at collecting samples and sequencing genomes but they seem utterly incompetent at analysing data and drawing the correct conclusions.

Yes, it's clear that ANF was the dominant ancestry group during the neolithic, but even after that Levantine movements into anatolia are zero or close to zero (limited maybe in small amounts to border regions) even by the bronze age. What we see quite plainly is widespread admixture between the Southern Caucasus and the Anatolian peninsula at the dawn of the copper age/end of the neolithic, which creates a profile intermediate between modern day Dodecanese Greeks and Armenians. This profile represents the Hittites, Luwians, Trojans and was also the profile that was influencing the more EEF like Minoans/Myceneans to make them further modern like with increased caucasian related ancestry. The Anatolian people, regardless of cultural context, retain this heavy ANF/Armenian Neolithic profile from the bronze age all the way into the middle ages until they are colonized by Turks which is actually quite remarkable.

The bigger question for me is how common Pinarbasi HG populations were in preneolithic anatolia and exactly how they came to be.
 
The bigger question for me is how common Pinarbasi HG populations were in preneolithic anatolia and exactly how they came to be.

They might be a very early split from core West Eurasians, if not the first. Their ultimate origin might lie in East Anatolia or the Caucasus from where they moved westwards.
 
They might be a very early split from core West Eurasians, if not the first. Their ultimate origin might lie in East Anatolia or the Caucasus from where they moved westwards.

Could they be modeled as Dzudzuana plus some sort of ghost WHG affinity? Perhaps input from an ancestral component of WHG? I notice Pinarbasi HG tends to cluster with EEFs more so than ANFs on PCA charts which suggests the higher WHG affinity.
 
Could they be modeled as Dzudzuana plus some sort of ghost WHG affinity? Perhaps input from an ancestral component of WHG? I notice Pinarbasi HG tends to cluster with EEFs more so than ANFs on PCA charts which suggests the higher WHG affinity.

To be frank, I am highly suspicious of PCA charts. Not saying they're BS but I'd advise anyone to take them with a grain of salt. There's a real plague of herd mentality in academia where models are copied, with little independent thinking involved. I'm not even sure there's much thinking done. But to come back to your question, the Reich paper (or was it Lazaridis'?) from 2018 claims that the paleolithic samples found in the Dzudzuana cave are more closely related to Anatolian farmers than they are to CHG. Since this is still during the LGM, I guess they meant Anatolian hunter-gatherers from whom the ANF derive almost all of their ancestry. Also postulated is a close relation between Dzudzuana and WHG of the Villabruna cluster from the post-glacial period. So all things considered, ANF were distant cousins of WHG. Previous publications claimed that, according to ADMIXTURE and qpAdm admixtools, ANF stood between WHG and Natufians. It's possible that some people misunderstood that and concluded that ANF were a mix of the two which is entirely false. Whatever affinities there are, they come from the fact that all these populations had Dzudzuana ancestry, which some authors interpret as core West Eurasian. Also discussed is the ostensible "Basal Eurasian" contribution to Dzudzuana but these BE ghosts stand on very shaky grounds in my opinion. It's just a layman's irrelevant opinion but what stands out to the eye is this ever-repeating pattern of inventing of phantoms in almost all scientific disciplines to fill in the gaps in presupposed models. This misguided approach is also largely responsible for the major stagnation and cosmological crisis in modern physics. Presupposed expectations (nature ought to bend to our models, not vice versa) and the fear of thinking independently because it may be damaging to one's academic career have been a serious obstacle to the advancement of science. A similar judgement can be passed about modern technology which is just variations on technology that was invented a long time ago. I remember how we used to laugh about the Japanese not inventing anything, just refining Western technology or making it more compact. Same can be said about the West today and even worse: we don't even make much technology nowadays.
 
To be frank, I am highly suspicious of PCA charts. Not saying they're BS but I'd advise anyone to take them with a grain of salt. There's a real plague of herd mentality in academia where models are copied, with little independent thinking involved. I'm not even sure there's much thinking done. But to come back to your question, the Reich paper (or was it Lazaridis'?) from 2018 claims that the paleolithic samples found in the Dzudzuana cave are more closely related to Anatolian farmers than they are to CHG. Since this is still during the LGM, I guess they meant Anatolian hunter-gatherers from whom the ANF derive almost all of their ancestry. Also postulated is a close relation between Dzudzuana and WHG of the Villabruna cluster from the post-glacial period. So all things considered, ANF were distant cousins of WHG. Previous publications claimed that, according to ADMIXTURE and qpAdm admixtools, ANF stood between WHG and Natufians. It's possible that some people misunderstood that and concluded that ANF were a mix of the two which is entirely false. Whatever affinities there are, they come from the fact that all these populations had Dzudzuana ancestry, which some authors interpret as core West Eurasian.

Dzudzuana being core west Eurasian makes sense to me in a lot of ways. It is effectively an intermediate population from which Taforalt admixture can create Natufians, ANE admixture can make later CHGs, and WHG could in potentially make Pinarbasi like HGs. Did all of these admixture events objectively happen to simplistically to create every one of these groups? Probably not and a good deal of this could just be genetic divergence which occurs naturally in isolated populations. But as a working hypothesis using Dzudzuana as a representation for early west Eurasians seems reasonable to me.



Also discussed is the ostensible "Basal Eurasian" contribution to Dzudzuana but these BE ghosts stand on very shaky grounds in my opinion. It's just a layman's irrelevant opinion but what stands out to the eye is this ever-repeating pattern of inventing of phantoms in almost all scientific disciplines to fill in the gaps in presupposed models. This misguided approach is also largely responsible for the major stagnation and cosmological crisis in modern physics. Presupposed expectations (nature ought to bend to our models, not vice versa) and the fear of thinking independently because it may be damaging to one's academic career have been a serious obstacle to the advancement of science.

I agree here as well. In my opinion we should stick to what we already know. Dzudzuana currently is the best match for representing the bulk of west eurasian ancestry and unless new evidence shows otherwise this should remain the presumption.

A similar judgement can be passed about modern technology which is just variations on technology that was invented a long time ago. I remember how we used to laugh about the Japanese not inventing anything, just refining Western technology or making it more compact. Same can be said about the West today and even worse: we don't even make much technology nowadays.

This is fairly off topic, but my perspective is a bit different than yours here. All technological innovation is simply the novel use case of preexisting principles (be these artificially engineered systems or naturally occurring). The refining of preexisting technology in of itself is an act of innovation, little different than the refining of principals already found in nature into controlled systems with dedicated use cases. At the moment technological innovation is advancing more rapidly than at any other point in history. To us it may appear redundant because we have the perspective of the prior waves of the industrial revolution to read about and study, but the reality of the fact is that the industrial revolution never actually ended. Lifestyles and problem solving techniques prior to the 18th century to now (~300 years) are vastly much more qualifiably separate to us at present than if we were to look at the entirety of classical antiquity up to the 17th century (2,400 years). We have the advantage of an enormous population size coupled with much more efficient resource extraction/refinement capabilities which has exponentially driven technological development compared to times past. This will begin to reduce as the overall human population shrinks due to falling birth rates in the near future.
 
To be frank, I am highly suspicious of PCA charts. Not saying they're BS but I'd advise anyone to take them with a grain of salt. There's a real plague of herd mentality in academia where models are copied, with little independent thinking involved. I'm not even sure there's much thinking done. But to come back to your question, the Reich paper (or was it Lazaridis'?) from 2018 claims that the paleolithic samples found in the Dzudzuana cave are more closely related to Anatolian farmers than they are to CHG. Since this is still during the LGM, I guess they meant Anatolian hunter-gatherers from whom the ANF derive almost all of their ancestry. Also postulated is a close relation between Dzudzuana and WHG of the Villabruna cluster from the post-glacial period. So all things considered, ANF were distant cousins of WHG. Previous publications claimed that, according to ADMIXTURE and qpAdm admixtools, ANF stood between WHG and Natufians. It's possible that some people misunderstood that and concluded that ANF were a mix of the two which is entirely false. Whatever affinities there are, they come from the fact that all these populations had Dzudzuana ancestry, which some authors interpret as core West Eurasian. Also discussed is the ostensible "Basal Eurasian" contribution to Dzudzuana but these BE ghosts stand on very shaky grounds in my opinion. It's just a layman's irrelevant opinion but what stands out to the eye is this ever-repeating pattern of inventing of phantoms in almost all scientific disciplines to fill in the gaps in presupposed models. This misguided approach is also largely responsible for the major stagnation and cosmological crisis in modern physics. Presupposed expectations (nature ought to bend to our models, not vice versa) and the fear of thinking independently because it may be damaging to one's academic career have been a serious obstacle to the advancement of science. A similar judgement can be passed about modern technology which is just variations on technology that was invented a long time ago. I remember how we used to laugh about the Japanese not inventing anything, just refining Western technology or making it more compact. Same can be said about the West today and even worse: we don't even make much technology nowadays.
I'm tempted to agree with your personal analysis of some academic trends...
 
I'm tempted to agree with your personal analysis of some academic trends...

The problem is also that there are too many scientists, so there's fierce competition on the job market. If you're fortunate enough to be employed at a university, you don't want to do anything that may endanger your position or future grants, so you stick with the mainstream. Of course, one can also go too far with "thinking out of the box" but I guess you catch my drift. Imagine if nobody ever dared say that Newton's definition of gravity is incomplete. Working on a problem forever is more to the benefit of one's career than solving it just like treating is more profitable for the pharma industry than finding a cure. What I'm trying to say is that we should always "follow the money" and ask if the motives behind published papers are purely scientific or are there other interests involved. This is not the scientists' fault. They are thrown into an economic environment where they have to compete for jobs and grants. Under such conditions scientific integrity often ends up thrown under the bus or it is at least not treated like a priority. There is no freedom of scientific inquiry where money is involved.
 
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To be frank, I am highly suspicious of PCA charts. Not saying they're BS but I'd advise anyone to take them with a grain of salt. There's a real plague of herd mentality in academia where models are copied, with little independent thinking involved. I'm not even sure there's much thinking done. But to come back to your question, the Reich paper (or was it Lazaridis'?) from 2018 claims that the paleolithic samples found in the Dzudzuana cave are more closely related to Anatolian farmers than they are to CHG. Since this is still during the LGM, I guess they meant Anatolian hunter-gatherers from whom the ANF derive almost all of their ancestry.

Also a slight but meaningful correction: Dzudzuana does indeed plot closer to Anatolian Neolithic Farmers than to the single Pinarbasi AHG we have, despite being temporally closer to Pinarbasi. This again would imply (but does not necessitate) that if Pinarbasi HG is representative of an AHG average then a European hunter gatherer like affininty was very slightly reduced over time in Anatolia (perhaps from direct dzudzuana like introgression). Another possibility is that the average actually did not change at all, but Pinarbasi HG simply happens to cluster closer towards the European HG end in comparison to other AHGs of the time. We don't have enough data to really infer a lot here, other than that all three of these populations (EEF, AHG, and Dzudzuana HG) are still rather closely related.
 
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