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

Gabriele Scorrano, Sofie Holtsmark Nielsen, Domenico Lo Vetro, Meaghan Mackie, Ashot Margaryan, Anna K. Fotakis, Cristina Martínez-Labarga, Pier Francesco Fabbri, Morten E. Allentoft, Marialetizia Carra, Fabio Martini, Olga Rickards, Jesper V. Olsen, Enrico Cappellini, Martin Sikora
doi: https://doi.org/10.1101/2021.12.08.471745
Gabriele Scorrano
1Section for Evolutionary Genomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
2Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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  • For correspondence: g.scorrano@sund.ku.dk ecappellini@sund.ku.dk martin.sikora@sund.ku.dk
Sofie Holtsmark Nielsen
2Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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Domenico Lo Vetro
3Dipartimento di Storia, Archeologia, Geografia, Arte e Spettacolo (SAGAS), University of Florence, Florence, Italy
4Museo e Istituto Fiorentino di Preistoria, Florence, Italy
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Meaghan Mackie
1Section for Evolutionary Genomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
5Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Ashot Margaryan
1Section for Evolutionary Genomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
6Center for Evolutionary Hologenomics, University of Copenhagen, Copenhagen, Denmark
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Anna K. Fotakis
1Section for Evolutionary Genomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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Cristina Martínez-Labarga
7Centro di Antropologia Molecolare per lo studio del DNA antico, Dipartimento di Biologia, University of Rome Tor Vergata, Rome, Italy
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Pier Francesco Fabbri
8Dipartimento di Beni Culturali, University of Salento, Lecce, Italy
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Morten E. Allentoft
2Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
9Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, Australia
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Marialetizia Carra
10DANTE: Diet and Ancient Technology Laboratory, Sapienza University of Rome, Rome, Italy
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Fabio Martini
3Dipartimento di Storia, Archeologia, Geografia, Arte e Spettacolo (SAGAS), University of Florence, Florence, Italy
4Museo e Istituto Fiorentino di Preistoria, Florence, Italy
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Olga Rickards
7Centro di Antropologia Molecolare per lo studio del DNA antico, Dipartimento di Biologia, University of Rome Tor Vergata, Rome, Italy
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Jesper V. Olsen
5Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Enrico Cappellini
1Section for Evolutionary Genomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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  • For correspondence: g.scorrano@sund.ku.dk ecappellini@sund.ku.dk martin.sikora@sund.ku.dk
Martin Sikora
2Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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  • For correspondence: g.scorrano@sund.ku.dk ecappellini@sund.ku.dk martin.sikora@sund.ku.dk
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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 past genetic diversity of our species. Here we present a “multi-omics” study, integrating genomic and proteomic analyses 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. Multi-omics analysis of dental calculus showed a diet rich of animal proteins which is also reflected on the oral microbiome composition. Our results demonstrate the power of using a multi-omics approach in the study of prehistoric human populations.

Competing Interest Statement

The authors have declared no competing interest.

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Genomic ancestry, diet and microbiomes of Upper Palaeolithic hunter-gatherers from San Teodoro cave (Sicily, Italy)
Gabriele Scorrano, Sofie Holtsmark Nielsen, Domenico Lo Vetro, Meaghan Mackie, Ashot Margaryan, Anna K. Fotakis, Cristina Martínez-Labarga, Pier Francesco Fabbri, Morten E. Allentoft, Marialetizia Carra, Fabio Martini, Olga Rickards, Jesper V. Olsen, Enrico Cappellini, Martin Sikora
bioRxiv 2021.12.08.471745; doi: https://doi.org/10.1101/2021.12.08.471745
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Genomic ancestry, diet and microbiomes of Upper Palaeolithic hunter-gatherers from San Teodoro cave (Sicily, Italy)
Gabriele Scorrano, Sofie Holtsmark Nielsen, Domenico Lo Vetro, Meaghan Mackie, Ashot Margaryan, Anna K. Fotakis, Cristina Martínez-Labarga, Pier Francesco Fabbri, Morten E. Allentoft, Marialetizia Carra, Fabio Martini, Olga Rickards, Jesper V. Olsen, Enrico Cappellini, Martin Sikora
bioRxiv 2021.12.08.471745; doi: https://doi.org/10.1101/2021.12.08.471745

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