Genomic and proteomic analysis of Palaeolithic, Neolithic and Bronze Age humans from Central-Southern Italy

Project Information

PALAEO-ENEO

Grant agreement ID: 751349

DOI

10.3030/751349

Project closed

EC signature date 23 March 2017

Start date 1 November 2017

End date 31 October 2019

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 200 194,80

EU contribution

€ 200 194,80

Coordinated by

KOBENHAVNS UNIVERSITET
Denmark

Periodic Reporting for period 1 - PALAEO-ENEO (Genomic and proteomic analysis of Palaeolithic, Neolithic and Bronze Age humans from Central-Southern Italy)

Reporting period: 2017-11-01 to 2019-10-31

Summary of the context and overall objectives of the project

To date, very fragmentary is the reconstruction of genomic profiles of ancient southern Europeans populations, due to their more challenging preservation. At the same time, which taxonomic groups, in the human oral microbiome, have been lost or gained with the introduction of agricolture is still no clear.
Accordingly, PALAEO-ENEO aimed at reconstruction of the human genomic profiles and at characterization of the oral microbiome of pre- and post-Neolithic anatomically modern humans from Central-Southern Italy, using genome-wide profiling and mass spectrometry-based proteomic analysis of skeletal remains and mineralised dental plaque (archaeological dental calculus). In particular all the research objectives of the project aimed to provide a more comprehensive knowledge about the Neolithic transition in Central-Southern Italy and they can be summarised as follow:
1. define the ancestral pre-Neolithic population in the Central-Southern Italy;
2. profile the Neolithic and post-Neolithic population in the same area;
3. test whether, and in which measure, there was an admixture between the hunter-gatherers and early farmers locally;
4. Metagenomic reconstruction of pre- and post-Neolithic oral microbiomes;
5. Metaproteomics reconstruction of pathophysiologic interactions between pre- and post-Neolithic oral microbiomes and their hosts, and diet reconstruction at a taxonomic resolution by proteomic approach.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

During the project, a total of 41 samples from 17 different sites and spanning from Palaeolithic to Chalcolithic periods from Central-Southern Italy have been analysed (Fig. 1).
All samples have undergone screening by shotgun sequencing approach and a total of 12 samples have been selected for deep sequencing.
The genetic results showed a genetic homogeneity among the Upper Palaeolithic Sicilian individuals suggesting the same population of origin associated to Villabruna Cluster, one of the genetic clusters that peopled Europe after the Last Glacial Maximum (LGM). Moreover, we showed a substructure of the Villabruna cluster and our human genetic results pointed out that Italian genetic cluster played a key role during the post-LGM resettlement of Europe. The genetic results from the Neolithic and Chalcolithic samples seems to be very informative about how the Neolithic transition occurred in the Mediterranean Basin. In particular, samples from Southern Italy showed a genetic profile different from the other Central Europe Early farmers.
Our data showed that the oral microbiome has changed through time, from a few species in Palaeolithic period to a more diversified microbiome with many different species, of which many causing periodontitis. Moreover, the data pointed out a clear diversification between the pre-Neolithic and post-Neolithic population, suggesting that the introduction of agriculture had a high impact in the ancient oral microbiome composition. Applying the proteomic approach on dental calculus, we also identified dietary proteins. The Palaeolithic samples showed high amount of collagen proteins pertinent to bovine, pig, equine; proteins matching with legumes were also confidently identified. Moreover, marine and freshwater fish exploitation was also attested. The presence of fishes proved the presence of the adequate technology and ability of this hunter-gatherer community to exploit marine and freshwater resources.
Concerning the Neolithic and post-Neolithic dental calculus results we found proteins matching with milk consumption in the Chalcolithic samples. This result is in agreement with the period analysed that can be described through the model of “Secondary Product Revolution” where the technology innovations led to a new revolution in food production, introducing and intensifying the exploitation of animal secondary products.
These results have already been disseminated to the scientific research community by national and international conferences and reported below.
These data are going to and will be published in several open access papers: Ancient biomolecules reveal ancestry, diet and microbiomes of Upper Palaeolithic hunter-gatherers from Sicily, Scorrano et al. is under revision of the Nature communication journal; Mesolithic, Neolithic and Chalcolithic human whole genome characterization of Southern Europe populations, Allentoft et al., is in preparation for high-impact journal such as Nature or Science; Proteomics analysis of oral dental calculus of Neolithic and Chalcolithic samples from Italy. Scorrano et al., is in preparation.
Finally, I also disseminated the results on public outreach: TOURISMA, 18th February 2018.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

The project outcomes are going to and will be published in several open access papers, as previously discussed:
1. Ancient biomolecules reveal ancestry, diet and microbiomes of Upper Palaeolithic hunter-gatherers from Sicily, Scorrano et al. is under revision of the Nature communication journal;
2. Mesolithic, Neolithic and Chalcolithic human whole genome characterization of Southern Europe populations, Allentoft et al., is in preparation for high-impact journal such as Nature or Science;
3. Proteomics analysis of oral dental calculus of Neolithic and Chalcolithic samples from Italy. Scorrano et al., is in preparation.
Results of the research have been presented at national/international conferences:
1. Scorrano G., et al., Multi-omics analysis of two Upper Palaeolithic individuals from Sicily. XXIII Congress of Italian Anthropological Association, Padua, 4th -6th September, 2019.
2. Scorrano G., et al, Components of human Palaeolithic diet identified using proteomic analysis of dental calculus from Southern Italy, Jena, 18th-21st September, 2018.
Moreover, I will present these results to the next American Association of Physical Anthropologist meeting that will take place in April 2020 in Los Angeles (CA), and to the next International Symposium on Biomolecular Archaeology that will take place in September 2020 in Toulouse (France).
Furthermore, I presented the results of this project on public outreach: TOURISMA.
I hereby confirm that I have always acknowledged EU funding of my work throughout the fellowship and will continue to do so when presenting or publishing work derived from results from this fellowship in the future.
This Marie Skłodowska-Curie action provided me the state of art training in the two most studied ancient biomolecules: DNA and proteins. The new expertise acquired during the project places me amongst the few individuals able to combine proteomic and genomic approaches, allowing me to be more competitive in the selection of new profiles in the molecular anthropological. As a matter of fact, after an initial collaboration with Prof. Eske Willerslev (Director of Centre for GeoGenetics) and Prof. Kristian Kristiansen (University of Gothenburg, Sweden) on Population genomics of the Viking world and on the European Bronze Age projects, I obtained a postdoc position at Lundbeck Foundation GeoGenetics Centre under the lead of Prof. Eske Willerslev one of the world leader in ancient genetic analysis.
Finally, the dynamic scientific environment of the Evogenomics and GeoGenetics sections and the interdisciplinary of the project allowed me to expand my network, consolidate the scientific relationship between Italy and Denmark and open new collaborations in Denmark and abroad.

Fig. 1: Geographic location and archaeological horizon and *number of the individuals analysed.