# Population Genetics > Paleogenetics > Paleolithic & Mesolithic >  Late Pleistocene genome suggests a local origin for the first farmers from Anatolia

## epoch

https://www.biorxiv.org/content/earl....full.pdf+html

This paper points to continuity, shows Basal Eurasian in Central Anatolia at 15.000 yeas ago, roughly 25%, shows some admixture from Iran and Levant, shows special affinity to Iron Gates HG's and rejects gene flow from Anatolia to S.E Europe on the basis of the absence of Basal Eurasian in the latter.

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## berun

which basal Eurasian proportion had de mean EEF?

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## MOESAN

Rejects gene flow at any time or only at the HG stage of Anatolia?
Because seemingly the Anatolian farmers coming to S-E Europe were a bunch of people from Catal Hyk at a well determined period, so a drifted little sample of people not representative of the mean Anatolian farmers. Or maybe I missed something.

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## ToBeOrNotToBe

> https://www.biorxiv.org/content/earl....full.pdf+html
> 
> This paper points to continuity, shows Basal Eurasian in Central Anatolia at 15.000 yeas ago, roughly 25%, shows some admixture from Iran and Levant, shows special affinity to Iron Gates HG's and rejects gene flow from Anatolia to S.E Europe on the basis of the absence of Basal Eurasian in the latter.


Interesting about the Iron Gates HGs - aren't they an R1b population?

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## Olympus Mons

_"We find that Iron Gates HG can be modeled as a three-way mixture ofNear-Eastern hunter-gatherers (25.8 ± 5.0 % AHG or 11.1 ± 2.2 % Natufian), WHG (62.9 ± 7.4It is made available under a CC-BY-NC-ND 4.0 International license.(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.bioRxiv preprint first posted online Sep. 20, 2018; doi: http://dx.doi.org/10.1101/422295. The copyright holder for this preprint8% or 78.0 ± 4.6 % respectively) and EHG (11.3 ± 3.3 % or 10.9 ± 3 % respectively)..."_


I always ask the same question - When this admix ( which is partly EHG) mixes with CHG will it not read misleadingly as Steppe component?

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## MOESAN

Old question, Olympus Mons.
EHG and CHG (or Neol Iran) admixture could be introduced independently in regions as it was already the case, firstable, among Steppes people before; but I suppose scholars have some clues which permit them to speak of 'steppe' EHG+CHG and not of something all. I avow I don't know how they manage this. (? some typical parts of each component always in correlation? distances?) -
auDNA classification can be weird: we have seen some "pure" components in some works broken down into more than one in other works...

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## bicicleur

the 15 ka HG C1a2 is from Pinarbasi, which is nowhere near Boncuklu or Tepecik-Ciftlik

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## bicicleur

> https://www.biorxiv.org/content/earl....full.pdf+html
> This paper points to continuity, shows Basal Eurasian in Central Anatolia at 15.000 yeas ago, roughly 25%, shows some admixture from Iran and Levant, shows special affinity to Iron Gates HG's and rejects gene flow from Anatolia to S.E Europe on the basis of the absence of Basal Eurasian in the latter.


'We also detect distinct genetic interactions between
the populations of central Anatolia and earlier farming centers to the east, during the late
Pleistocene/early Holocene as well as with European hunter-gatherers to the west during the Late
Pleistocene.'

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## Angela

> the 15 ka HG C1a2 is from Pinarbasi, which is nowhere near Boncuklu or Tepecik-Ciftlik


It certainly isn't close to them; it's practically on the Black Sea! So much for pre-publication "clues". :)

Well, we saw C1a2 in Europe as well, and one also later on during the Neolithic yes? The K2b isn't very common, is it? Interesting that they find genetic continuity from the hunter-gatherers to the farmers when so much of the uniparental signature was lost.

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## Angela

For ease of reference and clarity:
"Anatolia was home to some of the earliest farming communities. It has been long debated whether a migration of farming groups introduced agriculture to central Anatolia. Here, we report the first genome-wide data from a 15,000 year-old Anatolian hunter-gatherer and from seven Anatolian and Levantine early farmers. We find high genetic continuity between the hunter-gatherer and early farmers of Anatolia and detect two distinct incoming ancestries: an early Iranian/Caucasus related one and a later one linked to the ancient Levant. *Finally, we observe a genetic link between southern Europe and the Near East predating 15,000 years ago that extends to central Europe during the post-last-glacial maximum period.* Our results suggest a limited role of human migration in the emergence of agriculture in central Anatolia."

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## Angela

Their main point clearly is that "By analyzing this data, we find that the Anatolian hunter-gatherers are genetically distinct20 from other reported late Pleistocene populations and thus represent a previously undescribedpopulation. We reveal that Neolithic Anatolian populations derive a large fraction of theirancestry from the Epipaleolithic Anatolian population, suggesting farming was adopted locallyby the hunter-gatherers of central Anatolia."

More specifically:

"Accordingly, wefind an adequate two-way admixture model using qpAdm12 (χ2p = 0.158), in which *AHG derivesaround half of his ancestry from a Neolithic Levantine-related gene pool (48.0 ± 4.5 %; estimate± 1 SE) and the rest from the WHG-related one (tables S4 and S5).* These results support *a late15 Pleistocene presence of both ancestries in a mixed form in central Anatolia. Notably, the geneticconnection with the Levant predates the advent of farming in this region by at least fivemillennia and potentially correlates with evidence of human interactions between centralAnatolia and the Levant during the Epipalaeolithic13*.

In turn, AAF is slightly shifted upwards compared to AHG in the PCA, to the direction20 where ancient and modern Caucasus and Iranian groups are located. Likewise, when comparedto AHG by D(AAF, AHG; test, Mbuti),* the AAF early farmers show extra affinity with earlyHolocene populations from Iran or Caucasus and with present-day South Asians, who have alsobeen genetically linked with Iranian/Caucasus ancestry14, 15".*A mixture of AHG and Neolithic Iranians provides a good fit to AAF in our qpAdm modeling(χ2p = 0.296), in which* they derive most of their ancestry (89.7 ± 3.9 %) from a populationrelated to AHG (tables S4 and S6).* This suggests a long-term genetic stability in central Anatoliaover five millennia despite changes in climate and subsistence strategy.So, some small influence From Iran or Caucasus by the Holocene, but then the direction of gene flow changes.

"In contrast, we find that *the later ACF individuals share more alleles with the earlyHolocene Levantines than AAF do*, as shown by positive D(ACF, AAF; Natufian/Levant_N,Mbuti) ≥ 3.84 SE (Fig. 2B, fig. S3 and data table S3). Ancient Iran/Caucasus populations andcontemporary South Asians do not share more alleles with ACF (|D| < 3.3 SE). Likewise,qpAdm modeling suggests that *the AAF gene pool still constitutes more than 3/4 of the ancestry15 of ACF 2,000 years later (78.7 ± 3.5 %; tables S4 and S7) with additional ancestry well modeledby the Neolithic Levantines (χ2p = 0.115) but not by the Neolithic Iranians.*"

"In turn, *Levantineearly farmers* (Levant_Neol) that are temporally intermediate between AAF and ACF *could be20 modeled as a two-way mixture of Natufians and AHG or AAF (18.2 ± 6.4 % AHG or 21.3 ± 6.3% AAF ancestry*; tables S4 and S8 and data table S4), confirming previous reports of anAnatolian-like ancestry contributing to the Levantine Neolithic gene pool."

So, as they say: "detected gene flows support a reciprocal genetic exchange between the Levant and Anatoliaduring the early stages of the transition to farming".

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## Angela

In terms of affinity to Iron Gates HG:

"8. We find that *Iron Gates HG can be modeled as a three-way mixture ofNear-Eastern hunter-gatherers (25.8 ± 5.0 % AHG or 11.1 ± 2.2 % Natufian), WHG (62.9 ± 7.4 % or 78.0 ± 4.6 % respectively) and EHG (11.3 ± 3.3 % or 10.9 ± 3 %* respectively); (tables S4and S9). The affinity detected by the above D-statistic* can be explained by gene flow from NearEasternhunter-gatherers into the ancestors of Iron Gates or by a gene flow from a populationancestral to Iron Gates into the Near-Eastern hunter-gatherers as well as by a combination of5 both*. To distinguish the direction of the gene flow, we examined the Basal Eurasian ancestrycomponent (α), which is prevalent in the Near East 6but undetectable in European huntergatherers."

"Following a published approach6, we estimated *α to be 24.8 ± 5.5 % in AHG and38.5 ± 5.0 % in Natufians* (Fig. 3B, table S10), consistent with previous estimates for the latter6.Under the model of unidirectional gene flow from Anatolia to Europe, 6.4 % is expected for α of10 Iron Gates by calculating (% AHG in Iron Gates HG) × (α in AHG). *However, Iron Gates can bemodeled without any Basal Eurasian ancestry or with a non-significant proportion of 1.6 ± 2.8 %(Fig. 3B, table S10), suggesting that unidirectional gene flow from the Near East to Europe aloneis insufficient to explain the extra affinity between the Iron Gates HG and the Near-Easternhunter-gatherers. Thus, it is plausible to assume that prior to 15,000 years ago there was either a15 bidirectional gene flow between populations ancestral to Southeastern Europeans of the earlyHolocene and Anatolians of the late glacial or a dispersal of Southeastern Europeans into the Near East."

*However, what about the paper that found no Basal Eurasian there at that time?

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## Angela

> It certainly isn't close to them; it's practically on the Black Sea! So much for pre-publication "clues". :)
> 
> Well, we saw C1a2 in Europe as well, and one also later on during the Neolithic yes? The K2b isn't very common, is it? Interesting that they find genetic continuity from the hunter-gatherers to the farmers when so much of the uniparental signature was lost.


I think Bicicleur and I may have spoken too quickly. Yes, if you look up Pinarbasi, Turkey, it's on the Black Sea. However, their map of the samples shows Pinarbasi near Boncuklu.

There is also an ancient Pinarbasi in Konya province, indeed close to Boncuklu. So, Open Genomes was correct. Apologies.

See:
https://en.wikipedia.org/wiki/P%C4%B...G%C3%B6l%C3%BC

Here is a description of the site:
https://biaa.ac.uk/research/item/nam...si-excavations

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## bicicleur

> I think Bicicleur and I may have spoken too quickly. Yes, if you look up Pinarbasi, Turkey, it's on the Black Sea. However, their map of the samples shows Pinarbasi near Boncuklu.
> There is also an ancient Pinarbasi in Konya province, indeed close to Boncuklu. So, Open Genomes was correct. Apologies.
> See:
> https://en.wikipedia.org/wiki/P%C4%B...G%C3%B6l%C3%BC
> Here is a description of the site:
> https://biaa.ac.uk/research/item/nam...si-excavations


yes, I just arrived to the same conclusion
there are +/- 12 places named Pinarbasi in Turkey, it is this one :

https://www.google.com/maps/place/37...d33.0192?hl=en

thank you

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## bicicleur

blue eyes may have arrived into Anatolia from Europe prior to 15 ka

afaik the Konya plain was unihabited during LGM
I guess C1a2 came from west and G2a2 came from east
population was probably not dense when the met, possibly just a few founding individuals from both sides,
judging from TMRCA of both clades :

https://www.yfull.com/tree/C-V86/ 
assuming the C1a2 is V86, which split 41.5 ka from the La Brana branch

https://www.yfull.com/tree/G-L1259/
note that no other subclades of G have ever been observed in meso- or neolithic Central Anatolia

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## bicicleur

Angela, do you know more about Basal Eurasian in WHG, both before and in the Villabruna cluster?
And Basal Eurasian in Boncuklu?
Does the paper mention Basal Eurasian in the 15 ka AHG?

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## Angela

I don’t have access to my laptop so will respond with more depth later but aren’t they saying about 6.8 percent BE in the hunter gatherers? That’s in contrast to the slightly under 10 per cent found by Hamm in the farmers and the revised about 24 percent found by Lazaridis in, I think, Stuttgart. When I can I need to look at the Supplement closely.

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## Angela

> I don’t have access to my laptop so will respond with more depth later but aren’t they saying about 6.8 percent BE in the hunter gatherers? That’s in contrast to the slightly under 10 per cent found by Hamm in the farmers and the revised about 24 percent found by Lazaridis in, I think, Stuttgart. When I can I need to look at the Supplement closely.


That’s 1.6 percent BE in the Iron Gates HGs but they can be modeled without it. As for AHG they say 24.8 percent and 38.5 per cent in Natufians.

However, there is Hamm et al to consider with their figure of under 10 per cent.

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## ToBeOrNotToBe

Given the similarity of this to Iron Gates, is it possible that this was also R1b? I doubt it, but just putting speculation out there. Villabruna was also R1b.

I literally have close to zero idea why this is so significant though, I just haven't looked into it whatsoever to be frank.

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## Sile

> blue eyes may have arrived into Anatolia from Europe prior to 15 ka
> afaik the Konya plain was unihabited during LGM
> I guess C1a2 came from west and G2a2 came from east
> population was probably not dense when the met, possibly just a few founding individuals from both sides,
> judging from TMRCA of both clades :
> https://www.yfull.com/tree/C-V86/ 
> assuming the C1a2 is V86, which split 41.5 ka from the La Brana branch
> https://www.yfull.com/tree/G-L1259/
> note that no other subclades of G have ever been observed in meso- or neolithic Central Anatolia


this below are ancient samples of tdna and mtdna from early neolithic in malak Bulgaria

clearly there are many haplo links between anatolia and west coast bulgaria/romania
as for blue eyes.........the recent "*Ancient DNA from Chalcolithic Israel (Harney et al. 2018)*" paper has 80% plus of samples that where blue eyed and stated came from north anatolia, I doubt blue eyes formed in Europe

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## markod

Cool, Y-DNA C1a2, mtDNA K2b and a Venus figurine. I would be very surprised if this HG didn't have a bunch of rather recent ancestors who came from Europe. Most likely the eastern part of Europe.

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## Angela

Moesan, see post number 12. It isn't "rejected", precisely. This is why I prefer to first provide quotes from the authors and not interpretations of what they're saying. They see two possibilities during the epipaleolithic period: unidirectional flow from Europe to Anatolia, or bidirectional flow between the two areas. 

However, I'm unsure of where this stands given that a more recent paper found only 10% Basal Eurasian to speak of in the European farmers who were so similar to the Anatolian farmers. 

See:
John A. Kamm et al:

"Efficiently inferring the demographic history of many populations with allele count data"
https://www.biorxiv.org/content/bior...87268.full.pdf

"The sample frequency spectrum (SFS), or histogram of allele counts, is an important summary statistic in evolutionary biology, and is often used to infer the history of population size changes, migrations, and other demographic events affecting a set of populations. The expected multipopulation SFS under a given demographic model can be efficiently computed when the populations in the model are related by a tree, scaling to hundreds of populations. Admixture, back-migration, and introgression are common natural processes that violate the assumption of a tree-like population history, however, and until now the expected SFS could be computed for only a handful of populations when the demographic history is not a tree. In this article, we present a new method for efficiently computing the expected SFS and linear functionals of it, for demographies described by general directed acyclic graphs. This method can scale to more populations than previously possible for complex demographic histories including admixture. We apply our method to an 8-population SFS to estimate the timing and strength of a proposed "basal Eurasian" admixture event in human history. We implement and release our method in a new open-source software package momi2."

Lazaridis responded to it on his twitter account, but perhaps these authors didn't see it?

"*Iosif Lazaridis*‏ @iosif_lazaridis Mar 23More



A quick comment is that in Lazaridis et al. (2016) we present updated Basal Eurasian estimates for European farmers (Europe_EN) which is 23.9+/-3.8% (Table S4.9) which is closer to the 9.4% of the preprint than the original estimate for Stuttgart in the 2014 paper "

So, in March, it stood at 9.4% Basal Eurasian in EN versus 23.9%. 

Lazaridis went on to say:
"*osif Lazaridis*
‏ @iosif_lazaridis Mar 23More



Also, this estimate is subject to biases depending on whether EEF is really a mixture of just Basal Eurasian + WHG or it has additional non-Basal components (some of this is discussed in SI4). So, I don't feel strongly about the 23.9% number"


I love this guy, but perhaps because these are twitter comments, it's not clear to me how he feels about their method and their figure compared to his.

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