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Raveane A, Aneli S, Montinaro F, Athanasiadis G, Barlera S, Birolo G, Boncoraglio G, Di Blasio AM, Di Gaetano C, Pagani L, Parolo S, Paschou P, Piazza A, Stamatoyannopoulos G, Angius A, Brucato N, Cucca F, Hellenthal G, Mulas A, Peyret-Guzzon M, Zoledziewska M, Baali A, Bycroft C, Cherkaoui M, Chiaroni J, Di Cristofaro J, Dina C, Dugoujon JM, Galan P, Giemza J, Kivisild T, Mazieres S, Melhaoui M, Metspalu M, Myers S, Pereira L, Ricaut FX, Brisighelli F, Cardinali I, Grugni V, Lancioni H, Pascali VL, Torroni A, Semino O, Matullo G, Achilli A, Olivieri A, Capelli C. Population structure of modern-day Italians reveals patterns of ancient and archaic ancestries in Southern Europe. Sci Adv 2019; 5:eaaw3492. [PMID: 31517044 PMCID: PMC6726452 DOI: 10.1126/sciadv.aaw3492] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 04/10/2019] [Accepted: 08/06/2019] [Indexed: 05/10/2023]
Abstract
European populations display low genetic differentiation as the result of long-term blending of their ancient founding ancestries. However, it is unclear how the combination of ancient ancestries related to early foragers, Neolithic farmers, and Bronze Age nomadic pastoralists can explain the distribution of genetic variation across Europe. Populations in natural crossroads like the Italian peninsula are expected to recapitulate the continental diversity, but have been systematically understudied. Here, we characterize the ancestry profiles of Italian populations using a genome-wide dataset representative of modern and ancient samples from across Italy, Europe, and the rest of the world. Italian genomes capture several ancient signatures, including a non-steppe contribution derived ultimately from the Caucasus. Differences in ancestry composition, as the result of migration and admixture, have generated in Italy the largest degree of population structure detected so far in the continent, as well as shaping the amount of Neanderthal DNA in modern-day populations.
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Affiliation(s)
- A. Raveane
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
- Department of Zoology, University of Oxford, Oxford, UK
- Corresponding author. (A.R.); (S.A.); (F.M.); (C.C.)
| | - S. Aneli
- Department of Zoology, University of Oxford, Oxford, UK
- Department of Medical Sciences, University of Turin, Turin, Italy
- IIGM (Italian Institute for Genomic Medicine), Turin, Italy
- Corresponding author. (A.R.); (S.A.); (F.M.); (C.C.)
| | - F. Montinaro
- Department of Zoology, University of Oxford, Oxford, UK
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Corresponding author. (A.R.); (S.A.); (F.M.); (C.C.)
| | - G. Athanasiadis
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - S. Barlera
- Department of Cardiovascular Research, Istituto di Ricovero e Cura a Carattere Scientifico–Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - G. Birolo
- Department of Medical Sciences, University of Turin, Turin, Italy
- IIGM (Italian Institute for Genomic Medicine), Turin, Italy
| | - G. Boncoraglio
- Department of Cerebrovascular Diseases, IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
- PhD Program in Neuroscience, University Milano-Bicocca, Monza, Italy
| | - A. M. Di Blasio
- Istituto Auxologico Italiano, IRCCS, Centro di Ricerche e Tecnologie Biomediche, Milano, Italy
| | - C. Di Gaetano
- Department of Medical Sciences, University of Turin, Turin, Italy
- IIGM (Italian Institute for Genomic Medicine), Turin, Italy
| | - L. Pagani
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
- APE lab, Department of Biology, University of Padua, Padua, Italy
| | - S. Parolo
- Computational Biology Unit, Institute of Molecular Genetics, National Research Council, Pavia, Italy
| | - P. Paschou
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - A. Piazza
- Department of Medical Sciences, University of Turin, Turin, Italy
- Academy of Sciences, Turin, Italy
| | - G. Stamatoyannopoulos
- Department of Medicine and Genome Sciences, University of Washington, Seattle, WA, USA
| | - A. Angius
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - N. Brucato
- Evolutionary Medicine Group, Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, Toulouse, France
| | - F. Cucca
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - G. Hellenthal
- University College London Genetics Institute (UGI), University College London, London, UK
| | - A. Mulas
- Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Lanusei, Italy
| | - M. Peyret-Guzzon
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - M. Zoledziewska
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - A. Baali
- Faculté des Sciences Semlalia de Marrakech (FSSM), Université Cadi Ayyad, Marrakech, Morocco
| | - C. Bycroft
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - M. Cherkaoui
- Faculté des Sciences Semlalia de Marrakech (FSSM), Université Cadi Ayyad, Marrakech, Morocco
| | - J. Chiaroni
- Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France
- Etablissement Français du Sang PACA Corse, Biologie des Groupes Sanguins, Marseille, France
| | - J. Di Cristofaro
- Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France
- Etablissement Français du Sang PACA Corse, Biologie des Groupes Sanguins, Marseille, France
| | - C. Dina
- l’institut du thorax, INSERM, CNRS, University of Nantes, Nantes, France
| | - J. M. Dugoujon
- Evolutionary Medicine Group, Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, Toulouse, France
| | - P. Galan
- Equipe de Recherche en Epidémiologie Nutritionnelle (EREN), Centre de Recherche en Epidémiologie et Statistiques, Université Paris 13/Inserm U1153/Inra U1125/ Cnam, COMUE Sorbonne Paris Cité, F-93017 Bobigny, France
| | - J. Giemza
- l’institut du thorax, INSERM, CNRS, University of Nantes, Nantes, France
| | - T. Kivisild
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Department of Human Genetics, KU Leuven, Herestraat 49, box 604, Leuven 3000, Belgium
| | - S. Mazieres
- Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France
| | - M. Melhaoui
- Faculté des Sciences, Université Mohammed Premier, Oujda, Morocco
| | - M. Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - S. Myers
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - L. Pereira
- i3S–Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP–Instituto de Patologia e Imunologia Molecular, Universidade do Porto, Porto, Portugal
| | - F. X. Ricaut
- Evolutionary Medicine Group, Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, Toulouse, France
| | - F. Brisighelli
- Section of Legal Medicine, Institute of Public Health, Catholic University of the Sacred Heart, Rome, Italy
| | - I. Cardinali
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - V. Grugni
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - H. Lancioni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - V. L. Pascali
- Section of Legal Medicine, Institute of Public Health, Catholic University of the Sacred Heart, Rome, Italy
| | - A. Torroni
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - O. Semino
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - G. Matullo
- Department of Medical Sciences, University of Turin, Turin, Italy
- IIGM (Italian Institute for Genomic Medicine), Turin, Italy
| | - A. Achilli
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - A. Olivieri
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - C. Capelli
- Department of Zoology, University of Oxford, Oxford, UK
- Corresponding author. (A.R.); (S.A.); (F.M.); (C.C.)
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