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Population history of the Sardinian people inferred from whole-genome sequencing

View ORCID ProfileCharleston W K Chiang, Joseph H Marcus, Carlo Sidore, Hussein Al-Asadi, Magdalena Zoledziewska, Maristella Pitzalis, Fabio Busonero, Andrea Maschio, Giorgio Pistis, Maristella Steri, Andrea Angius, Kirk E Lohmueller, Goncalo R Abecasis, David Schlessinger, Francesco Cucca, John Novembre
doi: https://doi.org/10.1101/092148
Charleston W K Chiang
1Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Behavior, University of California, Los Angeles, Los Angeles, California, USA.
2Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, USA.
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Joseph H Marcus
3Department of Human Genetics, University of Chicago, Chicago, Illinois, USA.
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Carlo Sidore
4Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy.
5Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA.
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Hussein Al-Asadi
6Committee on Evolutionary Biology, University of Chicago, Chicago, Illinois, USA.
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Magdalena Zoledziewska
4Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy.
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Maristella Pitzalis
4Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy.
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Fabio Busonero
4Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy.
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Andrea Maschio
4Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy.
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Giorgio Pistis
4Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy.
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Maristella Steri
4Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy.
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Andrea Angius
4Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy.
7Center for Advanced Studies, Research and Development in Sardinia (CRS4), Advanced Genomics Computing Technology (AGCT) Program, Parco Scientifico e Tecnologico della Sardegna, Pula, Italy.
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Kirk E Lohmueller
2Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, USA.
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Goncalo R Abecasis
5Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA.
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David Schlessinger
8Laboratory of Genetics, National Institute on Aging, US National Institutes of Health, Baltimore, Maryland, USA.
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Francesco Cucca
4Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy.
9Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Sassari, Italy.
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John Novembre
3Department of Human Genetics, University of Chicago, Chicago, Illinois, USA.
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Abstract

The population of the Mediterranean island of Sardinia has made important contributions to genome-wide association studies of traits and diseases. The history of the Sardinian population has also been the focus of much research, and in recent ancient DNA (aDNA) studies, Sardinia has provided unique insight into the peopling of Europe and the spread of agriculture. In this study, we analyze whole-genome sequences of 3,514 Sardinians to address hypotheses regarding the founding of Sardinia and its relation to the peopling of Europe, including examining fine-scale substructure, population size history, and signals of admixture. We find the population of the mountainous Gennargentu region shows elevated genetic isolation with higher levels of ancestry associated with mainland Neolithic farmers and depleted ancestry associated with more recent Bronze Age Steppe migrations on the mainland. Notably, the Gennargentu region also has elevated levels of pre-Neolithic hunter-gatherer ancestry and increased affinity to Basque populations. Further, allele sharing with pre-Neolithic and Neolithic mainland populations is larger on the X chromosome compared to the autosome, providing evidence for a sex-biased demographic history in Sardinia. These results give new insight to the demography of ancestral Sardinians and help further the understanding of sharing of disease risk alleles between Sardinia and mainland populations.

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Posted December 07, 2016.
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Population history of the Sardinian people inferred from whole-genome sequencing
Charleston W K Chiang, Joseph H Marcus, Carlo Sidore, Hussein Al-Asadi, Magdalena Zoledziewska, Maristella Pitzalis, Fabio Busonero, Andrea Maschio, Giorgio Pistis, Maristella Steri, Andrea Angius, Kirk E Lohmueller, Goncalo R Abecasis, David Schlessinger, Francesco Cucca, John Novembre
bioRxiv 092148; doi: https://doi.org/10.1101/092148
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Population history of the Sardinian people inferred from whole-genome sequencing
Charleston W K Chiang, Joseph H Marcus, Carlo Sidore, Hussein Al-Asadi, Magdalena Zoledziewska, Maristella Pitzalis, Fabio Busonero, Andrea Maschio, Giorgio Pistis, Maristella Steri, Andrea Angius, Kirk E Lohmueller, Goncalo R Abecasis, David Schlessinger, Francesco Cucca, John Novembre
bioRxiv 092148; doi: https://doi.org/10.1101/092148

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