The mixed genetic origin of europe first farmers

[kingjohn]

Abstract
While the Neolithic expansion in Europe is well described archaeologically, the genetic origins of European first farmers and their affinities with local hunter-gatherers (HGs) remain unclear. To infer the demographic history of these populations, the genomes of 15 ancient individuals located between Western Anatolia and Southern Germany were sequenced to high quality, allowing us to perform population genomics analyses formerly restricted to modern genomes. We find that all European and Anatolian early farmers descend from the merging of a European and a Near Eastern group of HGs, possibly in the Near East, shortly after the Last Glacial Maximum (LGM). Western and Southeastern European HG are shown to split during the LGM, and share signals of a very strong LGM bottleneck that drastically reduced their genetic diversity. Early Neolithic Central Anatolians seem only indirectly related to ancestors of European farmers, who probably originated in the Near East and dispersed later on from the Aegean along the Danubian corridor following a stepwise demic process with only limited (2-6%) but additive input from local HGs. Our analyses provide a time frame and resolve the genetic origins of early European farmers. They highlight the impact of Late Pleistocene climatic fluctuations that caused the fragmentation, merging and reexpansion of human populations in SW Asia and Europe, and eventually led to the world's first agricultural populations.
Source:
https://www.biorxiv.org/content/10.1101/2020.11.23.394502v1?rss=1

P.s
From the new samples in this paper :
2 hunters belonged unsurprisingly to y haplogroups r1b1 and I2
The farmers belonged to y haplogroups G2, C1

The mtdna types that were found in this research:
U5a2a ×2( the 2 hunters)
K1a3 ×1
H3 ×1 ( nice in serbia lepinski vir it also surprised the author)
K1a4a1i ×1
K1a×1
K1a1×1
J1c6×1
U5a1c1×1
K1a2c×1
N1a1a1×1
W1-119×1
Hv-16311×1
T2e2×1
U5b2c1×1

 

[Pax Augusta]

I saw it yesterday, thanks for posting it. It is still preprint. What's really new?

 

[kingjohn]

I saw it yesterday, thanks for posting it. It is still preprint. What's really new?

you welcome,
yes look like pre- print
let us wait for published paper and release of the bam file
for pribislav anlaysis

here is what pribislav has to say about VLASA32 the r1b1 hunter from serbia

Iron Gates HGs are R1b-V2219 (xV88) .VLASA32 from this paper is L754 (xL389,V88), so most likely V2219 like the others we have so far.If he turns out to be V2219- he could be patrilinealy related to Villabruna ( see here ) .

​

source:
anthrogenica


p.s
what i think is new that this paper don't use basal eurasians in there model
and razib asked lazaridis about it

Originally Posted by Kristiina
If I have understood correctly their models (eg suppl material S53-S55), they use no Basal in their trees.



Razib asked Lazaridis and Excoffier about that on Twitter:

Originally Posted by Razib
no mention of 'basal eurasians' @iosif_lazaridis

(looked in supplements too)

Originally Posted by Excoffier
No need for it...

Originally Posted by Lazaridis
I haven't read the supplements yet (not as fast as you), but in the model of Fig. 3 there is no Ust'Ishim or Eastern non-Africans which would bring up the asymmetry. Certainly the model in which Loschbour and Iranian farmers are a simple split 23kya can't be taken at face value


​

 

[Pax Augusta]

you welcome,
yes look like pre- print
let us wait for published paper and release of the bam file
for pribislav anlaysis

Thanks, kingjohn.

 

[Angela]

The most incoherently written abstract I've seen in the last five years, and that's saying something.

Maybe after I read the supplement it will all make more sense.

 

[Angela]

What they're basically doing, at least in the paper itself, is looking only at the Hunter-Gatherer groups present around the time of the LGM in Europe and the Near East, and then trying to see where and when they admixed to produce "European farmers", and what that has to do with the spread of agriculture.

There were three groups in Europe: Loschbour and Bichon, separate from one another on a divided branch, and the Vlasic group in the Balkans/Aegean, including western Anatolia, corresponding to two western and one "central" refugia. As products of refugia they became inbred and highly differentiated. There were also three HG groups in the Near East: "one that later massively admixed with central HGs to become the ancestors of later 227 Anatolian and Aegean farmers, one leading to the ancestors of Iranian Neolithic farmers, and 228 one to Neolithic populations in the southern Levant (respectively east1, east2 and east3 on 229 Fig 4a). After the LGM, these HG populations re-expanded from their southern refugia probably due to improving climatic conditions37 230 , allowing previously separated central and 231 east1 refugial populations to overlap and admix 19 kya (Fig. 4b), and then to become a distinct 232 population from which Northwestern, Central Anatolian and European farmers would later 233 descend."

It seems that under the “Demic Diffusion Model” the “admixture” takes place in the Fertile Crescent. The only real difference between the two “Demic” versions which I can see is that in the first one the admixture could have taken place as early as the Younger Dryas, and in the second one the admixture took place only after the migration of locally descended people who had already reached the ceramic Neolithic stage.

I proposed the first version on this site years ago.

What I don’t see addressed is that the clear implication of version 1 is that agriculture thus spread by cultural diffusion perhaps as far as the whole Aegean region and into the Balkans. Doesn’t “real” “Demic diffusion” of agriculture require the migration of an already admixed group with a “Neolithic package”, even if they don’t have ceramics?

Their "Cultural Diffusion" Model has the genetic admixture taking place in the Aegean(including western Anatolia)/Balkans, with agriculture invented in the Fertile Crescent by different people and then "diffusing" culturally to the west. They concede it's a weak argument for the Aegean, Western Anatolia, Balkans, but see it as more possible for Central Anatolia and east and presumably Northeast from there.

Once they start looking at the spread from the Balkans to Austria, it is clearly demic diffusion, with some pick up of local HG ancestry along the way, but never increasing with time. Perhaps it was a situation like that in, say, South Africa, with farmer men blazing the trail taking HG women, but once farmer women followed it ceased. Otherwise, the percentages would have increased continuously. It's only much later on that there was significant admixture, perhaps reaching 20-25% depending on the area. Perhaps that's when the crashes started happening.

Confusingly enough, they later state the following, which at first glance seems to contradict the above:

"all Danubian early farmers can be traced back to a mixed population with substantial311 contributions from HGs as they appear later in SE Europe. Even though early farmers wererecognized to be genetically intermediate between other Near Eastern groups15 312 , or consideredas a mixture of other ancient21 or modern17 313 populations, this initial admixture signal remained314 hidden to previous approaches as it was eroded by later genetic drift (Fig. S50-51 and see315 below)."

First, ALL of these groups were hunter-gatherers until some of them learned how to farm. Second of all, what does the highlighted part mean? Do they mean what they call the "Central" Hunter Gatherers of the Balkans who actually occupied not only the Balkans but the Aegean and the western half of Anatolia and admixed with the "E1" Hunter Gatherers? Does that make the western Anatolian farmers who then went to Europe honorary Europeans or something? So the European farmers weren't so "foreign" after all?

Their preferred scenario, I guess.

To say I'm unimpressed is a vast understatement. We surmised much of this already. What does it change? If you go back far enough everybody mixed with everybody, even the Neanderthals.

They do also provide some tidbits, but all as expected.

"We find that the vast majority of early farmers in our dataset had intermediate to light skin 128 complexion, while HGs had a darker skin tone (Supp. Table 3). A dark (brown to black) hair 129 color was inferred for all but two samples, LEPE52 and VC3-2, who likely had light brown 130 hair. Eye color variation was similarly low, with all samples showing high probabilities for 131 brown eyes, except for two individuals of the Starčevo culture (STAR1 and VC3-2) which 132 were likely blue-eyed.

Based on polygenic scores, we show that early farmers are shorter than HGs (Student t-test, t 134 = -2.427, p-value = 0.027), and their stature declined between 8,300 and 7,000 BP (Pearson's r 135 = 0.6537, p-value < 0.008, Fig. S24), suggesting that selection for short stature occurred during 136 the Neolithic expansion along the Danubian corridor. 137 The allele associated with lactase persistence was not found in any of the analyzed ancient samples, consistent with an increase in frequency of these alleles at a later stage31 138 . However, 139 early farmers already show allele frequencies similar to contemporary Europeans for 6 out of 140 7 SNPs of the FADS1/2 gene complex, potentially selected in populations with plant-based diet32,33 141 (see Suppl. Information - Section 5, Table S7).

The change in skin color could be partly related to the change in diet.

 

[Angela]

Some more incoherence, this time on the Levant:

"Further support for the demic diffusion scenario comes from f-statistics showing Levantine269 populations to share more drift with Aegeans than with Central Anatolian Neolithic individuals270 (Fig. S57). This signal could either be due to some long distance gene flow between the271 Aegeans and the Levant, a higher level of central HG admixture observed in Boncuklu272 (Fig. S56), or a combination of i) an early migration of the Boncuklu HG ancestors from the273 Fertile Crescent to Central Anatolia before the Younger Dryas (Fig. 3a, 4c), ii) some gene flow274 between people from the Levant and the ancestors of Aegeans, who would have remained in275 the Fertile Crescent and only later migrated to the West. However, early farmers from the276 Aegean are rather heterogeneous in their levels of shared drift with several populations,including Levantine HGs and early Iranian farmers (Fig. S58), suggesting that the peopling of278 the Aegean was a complex process.

Look at what happens to the PCAs based on whether you use the neutrally evolving portion of the whole genomes

or one (Figure S19 - 2D-MDS)performed on the average nucleotide divergence (%XY ) matrix computedover the whole genome. Fig. S19b suggests strongest affinities of European Neolithic farmers with modernindividuals from Southern Europe (Crete, Greece, Italy, Albania, Spain) rather than with Sardinians,at odds with Fig. 2a and previous analyses based on the projections of ancient individuals onPrincipal Components computed from modern individuals only164. Note also that NW AnatolianEarly Neolithic individuals (AKT16 and Bar8) slightly diverge from the Neolithic cluster and are closer to modern individuals from Turkey and Bulgaria, thus showing some surprising geneticcontinuity across millennia within this region. CarsPas1 from England is also an outlier found inbetween Southern Europeans and a Bulgarian individual.

If that indicates continuity, then perhaps it's also indicated in Crete and Albania and even perhaps Tuscany and Bergamo? What would that do to the constant insistence of late "Levantine" gene flow into the Aegean. Crete is virtually part of the ancient European farmer group.

 

[Iulius]

What ever happened to the Dzudzuana paper and samples? I would imagine including them into this analysis would probably change everything.

How do they relate to these samples?

 

[binx]

It's probably my fault but I can't understand what this paper is trying to prove.

 

[MOESAN]

It's probably my fault but I can't understand what this paper is trying to prove.

I've the same painful feeling! I 've to read it again more carefully. ATW we knew some first farmers colonising Sth Europe came from diverse parts of the Fertile Crescent, someones by land and other maybe by coasts points leaping.

 

[ThirdTerm]

"all Danubian early farmers can be traced back to a mixed population with substantial311 contributions from HGs as they appear later in SE Europe. Even though early farmers were recognized to be genetically intermediate between other Near Eastern groups15 312 , or consideredas a mixture of other ancient21 or modern17 313 populations, this initial admixture signal remained314 hidden to previous approaches as it was eroded by later genetic drift (Fig. S50-51 and see315 below)."


First, ALL of these groups were hunter-gatherers until some of them learned how to farm. Second of all, what does the highlighted part mean? Do they mean what they call the "Central" Hunter Gatherers of the Balkans who actually occupied not only the Balkans but the Aegean and the western half of Anatolia and admixed with the "E1" Hunter Gatherers? Does that make the western Anatolian farmers who then went to Europe honorary Europeans or something? So the European farmers weren't so "foreign" after all?

Two Mesolithic hunter-gatherers (HGs) from Central Serbia are included in the study as the typical representatives of HGs (VLASA7, VLASA32), who carried I2 and R1b1. 13 samples of Early Neolithic farmers were mostly G2a men from NW Anatolia or the Aegean region, who migrated to the Balkans and admixed with the local European hunter-gatherers. Figure 3b suggests that they further migrated to the Danubian region (Lower Austria) and Southern Germany. The inferred rates of admixture with local Mesolithic populations (2-6%) are slightly lower than previously reported (3-9%). Figure 3a also shows that the Aegean region (admixed in Figure 4b) previously received substantial genetic contributions from central HGs in the Balkans around 19 kya. This scenario is plausible, considering the proximity of the two neighboring regions. Central HGs temporarily advanced to the Aegean region at the end of the LGM before retreating back to the Balkans by the early Neolithic period.

Altogether, this suggests that the LGM led to a fragmentation of HG populations in SW Asia and Europe with at least four genetically distinct groups: one related to Loschbour and Bichon (called west, subdivided into west1 and west2, based on the old divergence between Loschbour and Bichon branches), one related to the Danube Gorges Mesolithic samples (central), another one that later received the massive Central HG introgression (east1 then admixed), and a last one potentially further East (east2) related to WC1 (Fig. 3a, 4a, S34, S48, Supp. Table 4).

Figure 3 - Demographic scenario inferred from the sampled genomes and underlying genetic data. a: This demographic history was obtained by summarizing the best models of all tested scenarios. b: zoom-in on the red-square area in panel a. The X symbols indicate very strong bottlenecks that occurred on the HG ancestral branch before the divergence between Bichon-Loschbour and central European HGs and some 200 kya in the ancestral population. Only admixtures with point estimates ≥ 5% are represented with arrows (≥ 10% when arrows have a dark outline). c: MDS analyses performed on the neutrally evolving portion of the 17 ancient whole-genomes used in the demographic models (left) or on data simulated (right) according to the inferred ML parameters of the global scenario shown in panes a and b.

From an archaeological point of view, there have been a large number of proposed explanations for the introduction of Neolithic lifeways in Europe48. Our explicit modelling supports the simplest of all demic models, namely a gradual spread/progressive migration of early farmers originating in the wider Aegean region (NW Anatolia or Greece) and extending to Serbia along the Balkans and the so-called Danubian corridor, then to Hungary (usampled) and Austria, and eventually up to the Rhine valley in southwestern Germany (Fig. 1a, 4c). While this study focused on the Danubian or continental route of Neolithic expansion, we expect Impresso- and Cardial-related farmers who spread along the Mediterranean shoreline to have shared a similar genetic background in the Aegean14.

 

[Angela]

What ever happened to the Dzudzuana paper and samples? I would imagine including them into this analysis would probably change everything.

How do they relate to these samples?

I have no idea.

Using that sample, it seems to me, might change the modeling. After all, those 26,000 year old samples were pretty close to North West Anatolian farmers who appeared thousands of years later. According to Lazaridis much of the ancestry of the Dzudzuana samples was "related" to "Villabruna" type ancestry but he called the source the "Unknown Hunter Gatherer". I haven't yet combed through the whole Supplement. Is Villabruna closer to the Bichon/Loschbour branch or the Vlasic branch? At the time of the Lazaridis paper were the Balkan hunter-gatherer samples even available? Could the Dzudzuana paper's UHG be the Vlasic HG?

If so, then it would seem that the Vlasic HGs' range went right into the Caucasus, and perhaps just retreated into refugia areas in the Balkans and larger Aegean area during the LGM. It would also imply, wouldn't it, that the admixture between this HG who is "related" to the "western" HG branch admixed with E1 Near Eastern HGs long, long before the development of agriculture, which would provide support for the first of the versions of the demic diffusion model of this paper.

As for Basal Eurasian, it would have been part, presumably, of E1, since that's the HG with whom Vlasic mixed, and the Northwest Anatolian and EEF farmers have BE.

The issues of the impact of the Dzudzuana samples, BE, Ust Ishim, and ANE don't arise in the paper because the authors deliberately start their analysis in a much more recent time period, only using LGM period hunter-gatherers in Europe and the Near East. Those earlier samples were already "in" the genetic make-up of the LGM samples used in this paper.

Note also that they don't use later samples like EHG, which are much more recent.

Wouldn't their "new" PCA, which may indeed be an improvement over the older ones not using whole genomes and which projected the ancient samples onto modern ones, but what would happen if EHG samples had been included? Would the authors say all that variation is already in the LGM era samples?

Another point about the new PCA concerns the sample selection. I'd have to check the coordinates in the Supplement, but the map seems to imply they took the Sardinian samples from the central isolated region, so, the "oldest" area and yet they're very far from the EEF. Did they really take Tuscan samples from near Pisa or is it just a sloppy map? Notice the French samples are not from Lyon either, if you go by the map.

How much of the placement of the Sardinians is because of massive drift, given it's an island, and relatively untouched genetically for the last 1500 years? Or is it the additional Phoenician/Carthaginian and North African which might have filtered up even into the highlands?

How likely is it that there could have been massive infusions of genetic material into Italy starting with, say, the Gauls, and then through the Republic and Empire and even the Germanics, and still have Bergamo and especially Toscana wind up right back where they started, as very EEF like people? Can there be such a massive coincidence?

As you guys can see, I have mostly questions, not answers.

Also, couldn't they have thrown in some Southern Italian samples?

 

[Anfänger]

Vlasic HGs are I2 and R1b just like Villabrunna and Riparo Tagliente and the West HGs in this paper. East 1 HGs admixted with Vlasic HGs to produce the "Anatolian farmers" with G2 ? Wouldn't that imply that the admixture was mostly between Vlasic HG females and East 1 HG men with G2 ?

 

[Anfänger]

What ever happened to the Dzudzuana paper and samples? I would imagine including them into this analysis would probably change everything.

How do they relate to these samples?

Razib asked Lazaridis about the paper few months ago. Lazaridis replied "we have new samples, they waited for more than 20000 years, they can wait a little longer".

 

[Angela]

Vlasic HGs are I2 and R1b just like Villabrunna and Riparo Tagliente and the West HGs in this paper. East 1 HGs admixted with Vlasic HGs to produce the "Anatolian farmers" with G2 ? Wouldn't that imply that the admixture was mostly between Vlasic HG females and East 1 HG men with G2 ?

It's possible, as you say, that it might have been "mostly" Vlasic HG females with male G2 from refugia E1. Mostly is the operative word, perhaps; we have found I2 samples in Anatolia.

If, as I suspect, the admixture took place very early, when groups were quite small and then were isolated in separate refugia, it could simply be a function of drift, yes? The authors do make a point of saying that the groups in West Asia were not as "inbred". Still, although you can model Anatolian farmers, Levantine farmers, and Iranian farmers as having some similarities, they remain distinct groups, so there was some isolation. That story is in the distinct "y" lines.

 

[Anfänger]

Btw, the Vlasic HGs had brown and blue eyes. Maybe the 100% blue eyed WHGs are the result of a bottleneck ?