Genomic ancestry, diet and microbiomes of Upper Palaeolithic hunter-gatherers.

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Genomic ancestry, diet and microbiomes of Upper Palaeolithic hunter-gatherers from San Teodoro cave



Abstract

Recent improvements in the analysis of ancient biomolecules from human remains and associated dental calculus have provided new insights into the prehistoric diet and genetic diversity of our species. Here we present a multi-omics study, integrating metagenomic and proteomic analyses of dental calculus, and human ancient DNA analysis of the petrous bones of two post-Last Glacial Maximum (LGM) individuals from San Teodoro cave (Italy), to reconstruct their lifestyle and the post-LGM resettlement of Europe. Our analyses show genetic homogeneity in Sicily during the Palaeolithic, representing a hitherto unknown Italian genetic lineage within the previously identified Villabruna cluster. We argue that this lineage took refuge in Italy during the LGM, followed by a subsequent spread to central-western Europe. Analysis of dental calculus showed a diet rich in animal proteins which is also reflected on the oral microbiome composition. Our results demonstrate the power of this approach in the study of prehistoric humans and will enable future research to reach a more holistic understanding of the population dynamics and ecology.




Genetic structure of European Hunter-Gatherers

For the purpose of analysing the genetic diversity of European hunter-gatherers after the LGM, we merged the data from San Teodoro with a panel of previously published hunter-gatherer individuals (Palaeolithic and Mesolithic) from across Europe (Fig. 1a). To visualise the genetic structure of the ancient individuals, we performed multidimensional scaling on a distance matrix derived from pairwise identity-by-state (IBS) sharing of alleles among individuals (Fig. 1b, Supplementary Fig. 9). The two San Teodoro samples fell broadly within the genetic diversity of individuals from western and southern Europe, previously termed Western hunter-gatherers (WHG)19 (Fig. 1b, Supplementary Figs. 910). Within this group of individuals, San Teodoro clustered most closely with another Late Epigravettian individual from Sicily, Oriente C, and with the Late Upper Palaeolithic/Mesolithic individuals from Grotta Continenza (central Italy), indicating a common gene pool for post-LGM hunter-gatherers from the Italian peninsula from ~14,000 years ago onwards.


The clustering results are also confirmed by f4-statistics of the form f4(Mbuti, Test; SanTeodoro_LP.SG, DevilsCave_N.SG), which measures the excess of genetic drift a test individual shares with San Teodoro (from here on merged into a single population due to their high genetic similarity) compared to an outgroup (East Asian hunter-gatherers from Devil’s Gate cave). Results showed that WHG individuals, in particular those from the Italian peninsula, shared the highest amounts of genetic drift with San Teodoro. The highest affinity was observed for Oriente C (SIC2), an individual related to the same cultural sphere of San Teodoro (Late Epigravettian), with a similar age from the same geographic region (Sicily)20 (Fig. 1c, Supplementary Data 9).
Using f4-statistics of the form f4(Mbuti, Test; HG Italy, San_Teodoro_LP.SG), we next tested whether San Teodoro forms a clade with Italian hunter-gatherer groups, consisting of both Late Upper Palaeolithic (Oriente C, and Villabruna) and Late Upper Palaeolithic/Mesolithic (Continenza), to the exclusion of other test groups. While a clade-like relationship cannot be rejected for the Sicilian hunter-gatherer from Oriente C, significant statistics were observed in tests with the other two groups (Supplementary Fig. 11, Supplementary Data 10). For the central Italian individuals from Continenza, most post-LGM individuals showed significantly increased shared genetic drift compared to San Teodoro. The consistent magnitude of the statistics across individuals with a wide geographic distribution, and chrono-cultural differentiation, suggests possible gene flow between the ancestors of most post-LGM Europeans and Continenza, after their divergence from San Teodoro. Interestingly, the only individual with evidence for higher affinity with San Teodoro than with Continenza was the ~33,000-year-old pre-LGM individual Paglicci133 from Apulia in southern Italy (f4(Mbuti, Paglicci133; Italy_M.SG, San_Teodoro_LP.SG) = 0.003, Z = 2.6; Supplementary Figs. 9, 11). Paglicci 133 refers to Gravettian which is considered the cultural root (the Gravettian) from which the San Teodoro one (the Epigravettian) was derived in the following several millennia. This suggests possible gene flow involving ancestry related to pre-LGM hunter-gatherers in southern Italy, as previously observed on the Iberian Peninsula19, as a possible alternative explanation. A clade-like relationship was also rejected for the relationship of San Teodoro and the ~14,000-year-old northern Italian individual from Villabruna. In contrast to the results obtained with Continenza, in this analysis the individuals from western Europe mostly shared more genetic drift with San Teodoro, whereas individuals from eastern Europe shared more genetic drift with Villabruna (Supplementary Fig. 11, Supplementary Data 10). These results were also reflected in the genetic clustering, where Villabruna was shifted away from the Italian and west European individuals on a cline towards individuals from the Balkans (Iron Gates, Fig. 1b), suggesting further substructure among individuals of the Villabruna cluster.


The genetic diversity of European post-LGM hunter-gatherers has previously been described in terms of a west-to-east cline anchored by two major ancestry groups of western hunter-gatherers (WHG) and eastern hunter-gatherers (EHG)16, with some contributions from late Pleistocene hunter-gatherer ancestry in the Iberian Peninsula21. In the MDS in Fig. 1b, individuals were maximally differentiated in four distinct ancestry clusters, namely: (i) hunter-gatherers from the Italian peninsula (including San Teodoro), (ii) late Pleistocene hunter-gatherer ancestry (represented by Goyet Q-2), (iii) individuals from the Balkans (Iron Gates) and (iv) EHG from Russia. The remaining individuals were aligned across a number of distinct genetic clines, broadly related to their geographical location, including (Fig. 1b): (i) an Adriatic cline, linking the Italian peninsula to the Balkans; (ii) an Iberia late Pleistocene HG cline of Goyet Q-2 related ancestry in individuals from the Iberian peninsula; (iii) a Balkans-Ukraine cline and (iv) a NE Europe—Scandinavia—Russia cline, linking individuals from the Baltic to Scandinavia and EHG. Furthermore, we found evidence for temporal genetic structure within geographic regions. This was most notably at Iron Gates, where the earlier individuals from Serbia (before 9000 BP), together with the neighbouring individuals from Romania, form one of the four most differentiated clusters (Fig. 1b), whereas later individuals from Serbia (after 9000 BP) were shifted towards those from north-eastern Europe and the Baltics (Fig. 1b, Supplementary Fig. 12).

Motivated by these observations, we used qpAdm to infer ancestry proportions of European hunter-gatherers in a four-way model using representatives of the maximally differentiated genetic clusters as sources. The results recapitulated many of the features observed in the genetic clustering. In individuals from western Europe, ancestry related to Italian hunter-gatherers predominated, with varying contributions of late Pleistocene hunter-gatherer (Goyet Q-2) ancestry (Fig. 2, Supplementary Fig. 13, Supplementary Data 1114). Late Pleistocene ancestry peaked in the Iberian Peninsula, with inferred ancestry proportions as high as 71% (El Miron), consistent with previous results21. An apparent influx of Balkan hunter-gatherer related ancestry was observed in the two most recent individuals from northern Iberia (La Brana, Los Canes), suggesting gene flow between distinct ancestry groups towards the end of the hunter-gatherer dominion in western Europe22. In eastern Europe, ancestry related to Balkan hunter-gatherers was most abundant, with additional contributions of Italian or EHG ancestry, in line with the geographic origin of the individuals. Genetic continuity could be rejected for many of the later Balkan hunter-gatherers from Iron Gates, which showed evidence for admixture with groups harbouring both Italian- and Goyet Q-2-related ancestry (Supplementary Fig. 13; Supplementary Data 1114). Finally, EHG-related ancestry was found at highest proportions in individuals from Ukraine, as well as Scandinavian hunter-gatherers23. Once again, we observed temporal stratification in ancestry suggestive of local genetic transformations, with an increase in Balkan hunter-gatherer related ancestry in Ukrainian individuals after 10,000 BP16 (Supplementary Fig. 13). Taken together, these results document previously underappreciated complexity in the fine-scale genetic structure of post-LGM hunter-gatherers in Europe......



https://www.nature.com/articles/s42003-022-04190-2

 
I'm surprised that the Scandinavian HG are a mixture of Iron Gates with EHG, and not Italian LP with EHG.

Also, I wonder if the difference between Italian LP and Iron Gates HG could be some added Dzudzuana ancestry in the Iron Gates HG.
 
also surprising, 33 ka Paglicci is ancestral to LP Italy as opposed to nearby 29 ka Ostuni who belonged to the Vestonice cluster
 
I'm surprised that the Scandinavian HG are a mixture of Iron Gates with EHG, and not Italian LP with EHG.

One of the individuals from Gotland does have some Italian LP. All in all, a remarkable example of admixture between all groups.

6B74A5F3-93C0-4287-9327-1811AC7EC9FD.jpg
 
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One of the individuals from Gotland does have some Italian LP. All in all, a remarkable example of admixture between all groups.

View attachment 13681

they are lacking Goyet LP, which is Magdalenian

Hamburg culture were the Magdalenians that reached the Scandinavian icecaps, but they must have been completely whiped out by the incoming Ahrensburg people and the younger dryas climate change.
The Maglemosians, who arrived in southern Scandinavia after the younger dryas must have been related to the Iron Gates HG.

https://en.wikipedia.org/wiki/Hamburg_culture
https://en.wikipedia.org/wiki/Ahrensburg_culture
https://en.wikipedia.org/wiki/Maglemosian_culture

The Swiderian may have been a mixture of Iron Gates HG and Italian LP.

https://en.wikipedia.org/wiki/Swiderian_culture
 
We have known for some time that SHG was a mixture of EHG and WHG. Now it seems WHG in that was mostly Iron Gates… I wonder if they covered all the available Scandinavian HG samples.

Many HG sites are wihout human remains, though, so it remains inconclusive if the tools of a culture were accompanied by substantial migration or were the result of trading.
 
We have known for some time that SHG was a mixture of EHG and WHG. Now it seems WHG in that was mostly Iron Gates… I wonder if they covered all the available Scandinavian HG samples.

Many HG sites are wihout human remains, though, so it remains inconclusive if the tools of a culture were accompanied by substantial migration or were the result of trading.

Probably, the IronGatesHG ancestry already reached Scandinavia around the same time it settled in the Iron Gate area.
I suspect the Ahrensburg culture which arrived at the Scandinavian ice sheet ca 13 ka had only IronGatesHG ancestry.
It is well known that the mixture between the descendants of Ahrensburg culture (Komsa culture) with EHG from post-Swiderian Russia and Finland happened nearby the Varanger flord in the extreme north of Norway around 10 ka. That is where the SHG was formed. They returned south along the Norwegian coast and the through southern Scandinavia into the Baltic area (Kunda culture).

The first tribes that settled in the Iron Gate area were probably R1b-V2219. Their TMRCA is 15 ka. https://www.yfull.com/tree/R-V2219/
Villabruna 14 ka also had IronGatesHG ancestry which got mixed with Italy LP ancestry as his ancestors moved further west.
 
Goyet LP is Magdalenian, which originated somewhere in SW France, not in Iberia.
They were I* with autosomal Aurignacian DNA, their mtDNA was U8a.
I1* and I2* still had their original old Gravettian autosomal DNA. They split 27,5 ka.
I1* mixed with Aurignacian DNA in Iberia, 24 ka Cariguëla and 13 ka Bal051 were I1* with the mixed autosomal DNA.
I2* arrived in Italy and didn't mix with the locals. After the LGM they became dominant all over Italy.
I2 started to split 21,5 ka. In the end only I2a2-S2555* and I2a2-Y344225 remained in Italy.

https://www.yfull.com/tree/I-M436/
https://www.yfull.com/tree/I-M223/

Some of the I2 arrived in France and northern Iberia, they were the Azilians (Bichon, Iboussieres, Falkenstein, Bal03). They mixed with the Magdalenians and expanded north till the reached the ice sheets. Those were the Hamburg in northern Germany and Creswellian people in Great Britain. They hunted reindeer with the atlatl, just like the Magdalenians had done before them.
After the youngest dryas, 11,5 ka some of them moved eastward along the southern rim of the ice sheet. They were the Swiderians.

Some other I2 arrived at the Iron Gate area, which was occupied by the R1b-V2219 tribe since 15 ka.
There they mixed and learned about microliths and the bow and arrow.
Some of them turned north. They were the the Ahrensburg people. They arrived 13 ka at the ice sheet in northern Germany and southern Scandinavia. They whiped out the Hamburg tribes.
Their descendants were the Fosna-Hensbacka, Komsa and Maglemosian people.

Some of the Maglemosians crossed Doggerland to arrive in Great Britain around 10,5 ka and there they mixed with the Creswellians.
Before the arrival of the farmers, the Great Britain and Irish HG were this mixture.
Those Maglemosians were Y2a2-S2519. They were ancestral to I2a2b-L38 who later popped up in German Bell Beakers.

https://www.yfull.com/tree/I-M436/


The Komsa went up all the way north to the Varanger fjord where they mixed with EHG tribes.
Those mixed tribes were the SHG who turned back around 9,5 ka via the Norwegian coast into southern Scandinavia (Steigen, Hummervikjold >> Motala). The Scandinavian mainland was then still covered with an ice sheet.
Some of them arrived in Gotaland (Stora Forvar, Stora Bjers), others crossed the Baltic, they were the Kunda tribe.
In Zvejnieki, Latvia they mixed 8,4 ka with the R1b-FTA35755 tribe, who had autosomal Swiderian DNA.

https://www.yfull.com/tree/R-Y13200/


View attachment 13684
 
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The Ukrainian HG sample shows that WHG reached the Eastern side of the Carpathians. We should also assume EHG were roaming around the whole area from the Arctic across Baltic up to the Black Sea. Everywhere along the line there must have been contact with EHG.

We should see different R1a paternal lines to indicate multiple directions of migration.
 
they are lacking Goyet LP, which is Magdalenian

Hamburg culture were the Magdalenians that reached the Scandinavian icecaps, but they must have been completely whiped out by the incoming Ahrensburg people and the younger dryas climate change.

A pullback or wipeout due to the Younger Dryas cooling event does seem very likely.

Apparently the Goyet DNA re-emerged around the Pyrenees a few thousand years later. Their migration must have been constrained to the Atlantic seaboard later on.
 
I think the iron gates ancestry is originated from some people carrying I2* haplogroup because r1b is originated from ane
 

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