Population structure of modern-day Italians reveals patterns of ancient and archaic ancestries in Southern Europe

Anno:

2019

Population structure of modern-day Italians reveals patterns of ancient and archaic ancestries in Southern Europe

Raveane A1,2, Aneli S2,3,4, Montinaro F2,5, Athanasiadis G6, Barlera S7, Birolo G3,4, Boncoraglio G8,9, Di Blasio AM10, Di Gaetano C3,4, Pagani L5,11, Parolo S12, Paschou P13, Piazza A3,14, Stamatoyannopoulos G15, Angius A16, Brucato N17, Cucca F16, Hellenthal G18, Mulas A19, Peyret-Guzzon M20, Zoledziewska M16, Baali A21, Bycroft C20, Cherkaoui M21, Chiaroni J22,23, Di Cristofaro J22,23, Dina C24, Dugoujon JM17, Galan P25, Giemza J24, Kivisild T5,26, Mazieres S22, Melhaoui M27, Metspalu M5, Myers S20, Pereira L28,29, Ricaut FX17, Brisighelli F30, Cardinali I31, Grugni V1, Lancioni H31, Pascali VL30, Torroni A1, Semino O1, Matullo G3,4, Achilli A1, Olivieri A1, Capelli C2.

Sci Adv. 2019 Sep 4;5(9):eaaw3492. doi: 10.1126/sciadv.aaw3492. eCollection 2019 Sep. PMID:31517044

Author information

1: Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy.
2: Department of Zoology, University of Oxford, Oxford, UK.
3: Department of Medical Sciences, University of Turin, Turin, Italy.
4: IIGM (Italian Institute for Genomic Medicine), Turin, Italy.
5: Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia.
6: Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark.
7: Department of Cardiovascular Research, Istituto di Ricovero e Cura a Carattere Scientifico-Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy.
8: Department of Cerebrovascular Diseases, IRCCS Istituto Neurologico Carlo Besta, Milan, Italy.
9: PhD Program in Neuroscience, University Milano-Bicocca, Monza, Italy.
10: Istituto Auxologico Italiano, IRCCS, Centro di Ricerche e Tecnologie Biomediche, Milano, Italy.
11: APE lab, Department of Biology, University of Padua, Padua, Italy.
12: Computational Biology Unit, Institute of Molecular Genetics, National Research Council, Pavia, Italy.
13: Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
14: Academy of Sciences, Turin, Italy.
15: Department of Medicine and Genome Sciences, University of Washington, Seattle, WA, USA.
16: Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy.
17: Evolutionary Medicine Group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, Toulouse, France.
18: University College London Genetics Institute (UGI), University College London, London, UK.
19: Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Lanusei, Italy.
20: The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
21: Faculté des Sciences Semlalia de Marrakech (FSSM), Université Cadi Ayyad, Marrakech, Morocco.
22: Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France.
23: Etablissement Français du Sang PACA Corse, Biologie des Groupes Sanguins, Marseille, France.
24: l'institut du thorax, INSERM, CNRS, University of Nantes, Nantes, France.
25: 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.
26: Department of Human Genetics, KU Leuven, Herestraat 49, box 604, Leuven 3000, Belgium.
27: Faculté des Sciences, Université Mohammed Premier, Oujda, Morocco.
28: i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.
29: IPATIMUP-Instituto de Patologia e Imunologia Molecular, Universidade do Porto, Porto, Portugal.
30: Section of Legal Medicine, Institute of Public Health, Catholic University of the Sacred Heart, Rome, Italy.
31: Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy.

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.