Population structure of modern-day Italians reveals patterns of ancient and archaic ancestries in So

[Token]

European populations display low genetic diversity as the result of long term blending of the small number of ancient founding ancestries. However it is still unclear how the combination of ancient ancestries related to early European foragers, Neolithic farmers and Bronze Age nomadic pastoralists can fully explain genetic variation across Europe. Populations in natural crossroads like the Italian peninsula are expected to recapitulate the overall continental diversity, but to date have been systematically understudied. Here we characterised the ancestry profiles of modern-day Italian populations using a genome-wide dataset representative of modern and ancient samples from across Italy, Europe and the rest of the world. Italian genomes captured several ancient signatures, including a non-steppe related substantial ancestry contribution ultimately from the Caucasus. Differences in ancestry composition as the result of migration and admixture generated in Italy the largest degree of population structure detected so far in the continent and shaped the amount of Neanderthal DNA present in modern-day populations.

https://4.bp.blogspot.com/-soVFGe5618A/XBM67R367WI/AAAAAAAAHZM/25m7m7x9ttQy1J9gDpqFvUzOpTnIphVcACLcBGAs/s1600/Modern-day_Italians_Fig2.png

[J. Ketch]

Differences in ancestry composition as the result of migration and admixture generated in Italy the largest degree of population structure detected so far in the continent and shaped the amount of Neanderthal DNA present in modern-day populations.
Can someone translate this into English for me?

[Token]

Can someone translate this into English for me?

Italy is the country in Europe with the highest regional diversity, basically.

[gıulıoımpa]

i knew (correct me if i'm wrong ) that much of the present Neanderthal Heritage in Europe came out of Italy in a "second phase" after near complete annihilation in the rest of eruope to partially reconquer western europe and re- Neanderthalize it

[Kelmendasi]

The Caucasus admixture may be like the one in the Balkans. It seems to have arrived during the Bronze Age from west Asia and may be attributed to the arrival of certain J2a clade and perhaps some J1.

[Kelmendasi]

i knew (correct me if i'm wrong ) that much of the present Neanderthal Heritage in Europe came out of Italy in a "second phase" after near complete annihilation in the rest of eruope to partially reconquer western europe and re- Neanderthalize it
Reich suggests that Neanderthal ancestry in Europeans comes from intermixture between Homo Sapiens in the near east and Neanderthals that also inhabited the area. So you can assume that it was probably Neolithic farmers or other groups from west Asia that gave most of the Neanderthal admixture in Europeans. Paleolithic Europeans originally don't seem to have had Neanderthal admix as they moved into Europe before this mixing event, though I think it is logical to assume that later on they did mix. Oase sample from Romania seems to have had a lot of Neanderthal admix and predates Neolithic farmers, but, according to Reich this population group was a "dead end" and didn't influence modern Europeans.

[Kelmendasi]

Also seems that the Bell Beaker peoples in Sicily had a very small amount of Steppe admix, around 5%. Whilst the ones in northern Italy had a higher amount at around 14%. Though both groups seem to have had Anatolian Bronze Age admixture. The Bell Beaker groups from northern Italy plot quite close to modern north Italians, though the ones in Sicily plot with Neolithic European groups. Southern Italy showed the most CHG admix. North Italy always seems to have been different from the south.

[Token]

Reich suggests that Neanderthal ancestry in Europeans comes from intermixture between Homo Sapiens in the near east and Neanderthals that also inhabited the area. So you can assume that it was probably Neolithic farmers or other groups from west Asia that gave most of the Neanderthal admixture in Europeans. Paleolithic Europeans originally don't seem to have had Neanderthal admix as they moved into Europe before this mixing event, though I think it is logical to assume that later on they did mix. Oase sample from Romania seems to have had a lot of Neanderthal admix and predates Neolithic farmers, but, according to Reich this population group was a "dead end" and didn't influence modern Europeans.
Crown Eurasians actually had more Neanderthal than Dzudzuana (who accounts for basically the entire genepool of Anatolian farmers), including some Denisovan via East Asian admixture into Villabruna and ANE cluster. The explanation for this are the high levels of Basal Eurasian admixture - with negligible archaic admixture - of Anatolian/European farmers, that's why modern-day Northern Europeans got significantly more archaic admixture than EEF-rich Southern Europeans.

[Kelmendasi]

Crown Eurasians actually had more Neanderthal than Dzudzuana (who accounts for basically the entire genepool of Anatolian farmers), including some Denisovan via East Asian admixture into Villabruna and ANE cluster. The explanation for this are the high levels of Basal Eurasian admixture - with negligible archaic admixture - of Anatolian/European farmers, that's why modern-day Northern Europeans got significantly more archaic admixture than EEF-rich Southern Europeans.
Yh that would make sense. I guess that maybe it was another population group that moved into Europe from the near east rather than the Neolithic farmers. Reich also noted that Europeans have less Neanderthal admixture when compared to east Asians due to one of the ancestral groups of Europeans arriving before the mixture event in the near east, whilst the all the ancestral groups to east Asians took part in this mixture. What is your opinion on this?

[Token]

Yh that would make sense. I guess that maybe it was another population group that moved into Europe from the near east rather than the Neolithic farmers. Reich also noted that Europeans have less Neanderthal admixture when compared to east Asians due to one of the ancestral groups of Europeans arriving before the mixture event in the near east, whilst the all the ancestral groups to east Asians took part in this mixture. What is your opinion on this?

He might be referring to Basal Eurasians, though they only made their way into Europe with early farmers. Before that, only Iron Gates showed affinities to Dzudzuana. BE split off before Crown Eurasian expansions, just after the OOA bottleneck and before the Neanderthal inter-breeding event. They are so far the only Eurasian lineage (if they ever existed as a pure population) with negligible archaic admixture.

[Token]

Also seems that the Bell Beaker peoples in Sicily had a very small amount of Steppe admix, around 5%. Whilst the ones in northern Italy had a higher amount at around 14%. Though both groups seem to have had Anatolian Bronze Age admixture. The Bell Beaker groups from northern Italy plot quite close to modern north Italians, though the ones in Sicily plot with Neolithic European groups. Southern Italy showed the most CHG admix. North Italy always seems to have been different from the south.

The strong similarity between Parma Beaker and modern-day North Italians suggests that later Italic, Celtic, Roman and Germanic expansions made little to no impact on the local genepool, which is kinda hard for me to believe.

[gıulıoımpa]

Reich suggests that Neanderthal ancestry in Europeans comes from intermixture between Homo Sapiens in the near east and Neanderthals that also inhabited the area. So you can assume that it was probably Neolithic farmers or other groups from west Asia that gave most of the Neanderthal admixture in Europeans. Paleolithic Europeans originally don't seem to have had Neanderthal admix as they moved into Europe before this mixing event, though I think it is logical to assume that later on they did mix. Oase sample from Romania seems to have had a lot of Neanderthal admix and predates Neolithic farmers, but, according to Reich this population group was a "dead end" and didn't influence modern Europeans.Interesting , thanks a lot

Inviato dal mio SM-G389F utilizzando Tapatalk

[Kelmendasi]

He might be referring to Basal Eurasians, though they only made their way into Europe with early farmers. Before that, only Iron Gates showed affinities to Dzudzuana. BE split off before Crown Eurasian expansions, just after the OOA bottleneck and before the Neanderthal inter-breeding event. They are so far the only Eurasian lineage (if they ever existed as a pure population) with negligible archaic admixture.
This is what Reich says in his book, Who We Are And How We Got Here. The book was published in March 2018.

https://i.postimg.cc/QddGkWvY/IMG-2380.jpg

https://i.postimg.cc/KzLdv7gj/IMG-2381.jpg

https://i.postimg.cc/Bb75rkQK/IMG-2382.jpg

https://i.postimg.cc/Yqjz6rbf/IMG-2383.jpg

He says that pre-farming Europeans actually had about as much Neanderthal admix as modern east Asians. So Neanderthal admixture didn't come with EEF peoples it seems.

[Token]

This is what Reich says in his book, Who We Are And How We Got Here. The book was published in March 2018.

He says that pre-farming Europeans actually had about as much Neanderthal admix as modern east Asians. So Neanderthal admixture didn't come with EEF peoples it seems.

Yeah, basically what i said to you: Upper Paleolithic Europeans had a lot of Neanderthal admixture which was subsequently diluted by the Basal Eurasian admixture mediated by European farmers. The 'group of non-Africans who separated prior to the admixture with Neanderthals' he is referring to are the Basal Eurasians.

[nightrider+]

.

https://4.bp.blogspot.com/-soVFGe5618A/XBM67R367WI/AAAAAAAAHZM/25m7m7x9ttQy1J9gDpqFvUzOpTnIphVcACLcBGAs/s1600/Modern-day_Italians_Fig2.png

Interesting. Some people claim that Iberians are more steppe than Greeks and Balkanites because of the R1b.

[Token]

Interesting. Some people claim that Iberians are more steppe than Greeks and Balkanites because of the R1b.

Their CP/NNLS estimates are very off. 25% EHG - about the same level as North Italians - in Northern Europe with no CHG at all, only 30% Steppe_MLBA in Northwestern Europe, 50% EHG in Eastern Europe, EHG in Spaniards peaking in Basques. Horrible fits to be honest.

https://i.imgur.com/EV1fSpy.png

[IncelSlayer]

Instead of wasting time&money with those bullshit tests, they should just test the thousands of victims from Vesuvius :bored:

[Aren]

Nothing we didn't already know. There's BA Anatolian admixture across most of Southern Europe, including in Northern Italians and Iberians. Some extreme southern Euros such as Southern Italians and Greek Islanders also have BA-IA Levantine input.
Only interesting thing is that we'll get more academic samples of modern day Italians by region once the paper is out.

[Token]

Nothing we didn't already know. There's BA Anatolian admixture across most of Southern Europe, including in Northern Italians and Iberians. Some extreme southern Euros such as Southern Italians and Greek Islanders also have BA-IA Levantine input.
Only interesting thing is that we'll get more academic samples of modern day Italians by region once the paper is out.

Their ChromoPainter looks very strange. Northern Italy as much SBA as Northwestern Europe; Northern Europe as much SBA as the Balkans; no CHG in Northern Europe. There is something wrong with these runs.

[nightrider+]

Their ChromoPainter looks very strange. Northern Italy as much SBA as Northwestern Europe; Northern Europe as much SBA as the Balkans; no CHG in Northern Europe. There is something wrong with these runs.If SBA is Yamnaya, it doesn't seem that off, and Northern Europe would have no CHG if it wasn't for the steppe people.

[Token]

If SBA is Yamnaya, it doesn't seem that off, and Northern Europe would have no CHG if it wasn't for the steppe people.

And that is the major problem. When they take out SBA as reference in their admixture runs there is still no CHG, only EHG, which is counterlogical.

[nightrider+]

And that is the major problem. When they take out SBA as reference in their admixture runs there is still no CHG, only EHG, which is counterlogical.It gets absorbed by the Anatolian neolithic which is interesting. Admixture runs should never be taken out of context. They obviously wanted to demonstrate how much post neolithic CHG Italy has.

[Token]

It gets absorbed by the Anatolian neolithic which is interesting. Admixture runs should never be taken out of context. They obviously wanted to demonstrate how much post neolithic CHG Italy has.

Anatolia Neolithic has nothing to do with CHG though. At least the figures for Italy seems coherent, if this is the context you are talking about. Everything else looks like bullshit.

[nightrider+]

Anatolia Neolithic has nothing to do with CHG though. At least the figures for Italy seems coherent, if this is the context you are talking about. Everything else looks like bullshit.Everything has to do with anything in genetics.

http://eurogenes.blogspot.com/2016/02/chg-admixture-in-early-western.html?m=1

[Token]

Everything has to do with anything in genetics.

http://eurogenes.blogspot.com/2016/02/chg-admixture-in-early-western.html?m=1

This is old story. Only one clearly outlier Anatolian farmer with J2a shows significant level (one digits) of CHG, and it is not even proper CHG but more than likely something related to Tepecik-Ciftlik. CHG became widespread among Anatolians during the Middle Bronze Age. Before that, only at trace amounts at best.

[nightrider+]

This is old story. Only one clearly outlier Anatolian farmer with J2a shows significant level (one digits) of CHG, and it is not even proper CHG but more than likely something related to Tepecik-Ciftlik. CHG became widespread among Anatolians during the Middle Bronze Age. Before that, only at trace amounts at best.http://eurogenes.blogspot.com/2016/02/chg-admixture-in-early-western.html?showComment=1455196923808&m=1#c5660767877194660552

It's probably not direct ancestry but something is there that differentiates them. That's why I said it's interesting that the chg seems to be ansorbed by an in that run.

[Bogdan]

This makes sense. You see a lot of variation among Italians.

[Ibericus]

PCA plot :

https://i.ibb.co/m91RhwH/pca.png

[Token]

PCA plot :


Northeastern Italy clearly shifting towards Eastern Europe, Piedmont towards Northwestern Europe. Both of these clusters (NItaly6 and NItaly1) got 0% Anatolian admixuture, which might have been diluted by contacts with Central European pops similar to what occured with South Slavs. Probably contacts with Slovenians and French respectively.

[Token]

The pie charts shows Veneto as a perfect intermediate between Emilia-Romagna and Friuli.

[Ibericus]

Northeastern Italy clearly shifting towards Eastern Europe, Piedmont towards Northwestern Europe. Both of these clusters (NItaly6 and NItaly1) got 0% Anatolian admixuture, which might have been diluted by contacts with Central European pops similar to what occured with South Slavs. Probably contacts with Slovenians and French respectively.

No, Piedmont/Aosta samples are getting close to Iberians (Western EUrope in the PCA) and NW EUrope 1 which is France.

[Lucas]

No, Piedmont/Aosta samples are getting close to Iberians (Western EUrope in the PCA) and NW EUrope 1 which is France.

True. In every serious calc.

[kaltar]

PCA plot :

Other PCAs

https://i.ibb.co/GQRvh5J/PCA1-1.jpg

https://i.ibb.co/zPWXGRp/PCA1-2.jpg

[Token]

No, Piedmont/Aosta samples are getting close to Iberians (Western EUrope in the PCA) and NW EUrope 1 which is France.
'No' what? That is exactly what i said, France is Northwestern Europe and Piedmont is shifting towards France, not towards Iberians. LOL

[Ibericus]

'No' what? That is exactly what i said, France is Northwestern Europe and Piedmont is shifting towards France, not towards Iberians. LOL

Man you are blind, cause they are also clearly touching part of the iberian cluter (represented as 'Western EUrope')

[Sikeliot]

The map clearly shows Italy on a gradient from being like West-Central Europeans in the north, to being close to Middle Easterners in the south -- if there were Cypriots on the PCA plot, they'd bridge the gap between southerners and Middle Eastern.

Also, north Italy appears far more diverse and varied genetically than the south!

[Sikeliot]

Some other important pieces from the study:


Italian clusters separated into three main groups: Sardinia, Northern (North/Central-North Italy) and Southern Italy (South/Central-South Italy and Sicily); the former two were close to populations originally from Western Europe, while the latter was in proximity of Middle East groups (Fig. 1A, fig. S2, data file S2). The cluster-composition of the administrative regions of Italy provided further evidence for geographic structuring (Fig. 1B) with the separation between Northern and Southern areas being shifted North along the peninsula; the affinity to Western and Middle Eastern populations was also evident in the haplotype-based PCA (Fig. 1C), allele frequency PCA (fig. S3) and the ADMIXTURE analysis (fig. S4).


Clusters within Italy were significantly more different from each other than within any other country here included


In the Ultimate analysis, all the Italian clusters were characterised by relatively high amounts of Anatolian Neolithic (AN), ranging between 56% (SItaly1) and 72% (NItaly4), distributed along a North-South cline (Spearman ρ = 0.52, p-value < 0.05; Fig. 2A-C, fig. S8A),with Sardinians showing values above 80%. A closer affinity of Northern Italian than Southern Italian clusters to AN was also supported by D-statistics (fig. S10). The remaining ancestry was mainly assigned to WHG (Western Hunter-Gatherer), CHG and EHG. In particular, the first two components were more present in populations from the South (higher estimates in SItaly1 ~13% and SItaly3 ~ 24% for WHG and CHG respectively), while the latter was more common in Northern clusters (NItaly6 = 15%). These observations suggest the existence of different secondary sources contributions to the two edges of the peninsulas, with the North affected more by EHG-related populations and the South affected more by CHG-related groups. Iran Neolithic (IN) ancestry was detected in Europe only in Southern Italy.


SBA (Steppe Bronze Age) contribution ranged between 33% in the North and 6% in the South of Italy


We therefore speculate that our approach might in general underestimate the presence of CHG across the continent; however, we note that even considering this scenario, the excess of Caucasus related ancestry detected in the South of the European continent, and in Southern Italy in particular, is striking and unexplained by currently proposed models for the peopling of the continent.


We also noted that in the Balkan peninsula signatures related to ABA (Anatolian Bronze Age) were present but less evident than in Southern Italy across modern-day populations, possibly masked by historical contributions from Central Europe


North African contributions, ranging between 3.8% (SCItaly1) to 14.5% (SItaly1) became evident when combinations of five sources were tested.


The Bell Beaker samples of Northern Italy (2,200-1,930 BCE) were modelled as ABA and AN + SBA and WHG, although ABA was characterised by large standard errors but the detection of Steppe ancestry, at 14%, was more robust. On the other hand Bell Beaker samples from Sicily (2,500-1,900 BCE) were modelled almost exclusively as ABA, with less than 5% SBA.