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Population history from the Neolithic to present on the Mediterranean island of Sardinia: An ancient DNA perspective

View ORCID ProfileJoseph H. Marcus, View ORCID ProfileCosimo Posth, View ORCID ProfileHarald Ringbauer, Luca Lai, View ORCID ProfileRobin Skeates, View ORCID ProfileCarlo Sidore, Jessica Beckett, Anja Furtwängler, Anna Olivieri, View ORCID ProfileCharleston Chiang, View ORCID ProfileHussein Al-Asadi, View ORCID ProfileKushal Dey, Tyler A. Joseph, View ORCID ProfileClio Der Sarkissian, Rita Radzevičiūtė, Maria Giuseppina Gradoli, View ORCID ProfileWolfgang Haak, David Reich, David Schlessinger, View ORCID ProfileFrancesco Cucca, Johannes Krause, View ORCID ProfileJohn Novembre
doi: https://doi.org/10.1101/583104
Joseph H. Marcus
1Department of Human Genetics, University of Chicago, Chicago, IL, USA.
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Cosimo Posth
2Max Planck Institute for the Science of Human History, Jena, Germany.
3Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany.
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Harald Ringbauer
1Department of Human Genetics, University of Chicago, Chicago, IL, USA.
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Luca Lai
4Department of Anthropology, University of South Florida, Tampa, FL, USA.
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Robin Skeates
5Department of Archaeology, Durham University, Durham, United Kingdom.
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Carlo Sidore
6Istituto di Ricerca Genetica e Biomedica - CNR, Cagliari, Italy.
7Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy.
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Jessica Beckett
8Private contractor, Cagliari, Sardinia.
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Anja Furtwängler
3Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany.
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Anna Olivieri
9Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, Pavia, Italy.
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Charleston Chiang
10Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
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Hussein Al-Asadi
11Department of Statistics, University of Chicago, Chicago, IL, USA.
12Committee on Evolutionary Biology, University of Chicago, Chicago, IL, USA.
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Kushal Dey
13Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts 02115, USA.
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Tyler A. Joseph
14Department of Computer Science, Columbia University, New York, NY, USA.
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Clio Der Sarkissian
15Team AGES Laboratory AMIS Faculté de Médecine de Purpan, Toulouse, France.
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Rita Radzevičiūtė
2Max Planck Institute for the Science of Human History, Jena, Germany.
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Maria Giuseppina Gradoli
16School of Archaeology and Ancient History, University of Leicester, Leicester, United Kingdom.
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Wolfgang Haak
2Max Planck Institute for the Science of Human History, Jena, Germany.
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David Reich
17Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
18Broad Institute of Harvard and MIT, Cambridge, MA, USA.
19Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA.
20Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean
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David Schlessinger
21Laboratory of Genetics, NIA, NIH, Baltimore, MD, USA.
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Francesco Cucca
6Istituto di Ricerca Genetica e Biomedica - CNR, Cagliari, Italy.
7Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy.
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Johannes Krause
2Max Planck Institute for the Science of Human History, Jena, Germany.
3Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany.
20Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean
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John Novembre
1Department of Human Genetics, University of Chicago, Chicago, IL, USA.
22Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA.
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Abstract

Recent ancient DNA studies of western Eurasia have revealed a dynamic history of admixture, with evidence for major migrations during the Neolithic and Bronze Age. The population of the Mediterranean island of Sardinia has been notable in these studies – Neolithic individuals from mainland Europe cluster more closely with Sardinian individuals than with all other present-day Europeans. The current model to explain this result is that Sardinia received an initial influx of Neolithic ancestry and then remained relatively isolated from expansions in the later Neolithic and Bronze Age that took place in continental Europe. To test this model, we generated genome-wide capture data (approximately 1.2 million variants) for 43 ancient Sardinian individuals spanning the Neolithic through the Bronze Age, including individuals from Sardinia’s Nuragic culture, which is known for the construction of numerous large stone towers throughout the island. We analyze these new samples in the context of previously generated genome-wide ancient DNA data from 972 ancient individuals across western Eurasia and whole-genome sequence data from approximately 1,500 modern individuals from Sardinia. The ancient Sardinian individuals show a strong affinity to western Mediterranean Neolithic populations and we infer a high degree of genetic continuity on the island from the Neolithic (around fifth millennium BCE) through the Nuragic period (second millennium BCE). In particular, during the Bronze Age in Sardinia, we do not find significant levels of the “Steppe” ancestry that was spreading in many other parts of Europe at that time. We also characterize subsequent genetic influx between the Nuragic period and the present. We detect novel, modest signals of admixture between 1,000 BCE and present-day, from ancestry sources in the eastern and northern Mediterranean. Within Sardinia, we confirm that populations from the more geographically isolated mountainous provinces have experienced elevated levels of genetic drift and that northern and southwestern regions of the island received more gene flow from outside Sardinia. Overall, our genetic analysis sheds new light on the origin of Neolithic settlement on Sardinia, reinforces models of genetic continuity on the island, and provides enhanced power to detect post-Bronze-Age gene flow. Together, these findings offer a refined demographic model for future medical genetic studies in Sardinia.

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Posted March 21, 2019.
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Population history from the Neolithic to present on the Mediterranean island of Sardinia: An ancient DNA perspective
Joseph H. Marcus, Cosimo Posth, Harald Ringbauer, Luca Lai, Robin Skeates, Carlo Sidore, Jessica Beckett, Anja Furtwängler, Anna Olivieri, Charleston Chiang, Hussein Al-Asadi, Kushal Dey, Tyler A. Joseph, Clio Der Sarkissian, Rita Radzevičiūtė, Maria Giuseppina Gradoli, Wolfgang Haak, David Reich, David Schlessinger, Francesco Cucca, Johannes Krause, John Novembre
bioRxiv 583104; doi: https://doi.org/10.1101/583104
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Population history from the Neolithic to present on the Mediterranean island of Sardinia: An ancient DNA perspective
Joseph H. Marcus, Cosimo Posth, Harald Ringbauer, Luca Lai, Robin Skeates, Carlo Sidore, Jessica Beckett, Anja Furtwängler, Anna Olivieri, Charleston Chiang, Hussein Al-Asadi, Kushal Dey, Tyler A. Joseph, Clio Der Sarkissian, Rita Radzevičiūtė, Maria Giuseppina Gradoli, Wolfgang Haak, David Reich, David Schlessinger, Francesco Cucca, Johannes Krause, John Novembre
bioRxiv 583104; doi: https://doi.org/10.1101/583104

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