Population structure of modern-day Italians reveals patterns of ancient and archaic ancestries in Southern Europe
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. ; The Leverhulme Trust (F.M. and C.C.); the Italian Ministry of Education, University and Research (MIUR): "Progetti Futuro in Ricerca 2012" (RBFR126B8I) (A.O. and A.A); the "Dipartimenti di Eccellenza (2018–2022)" [Department of Medical Sciences of Turin (G.M.); Department of Biology and Biotechnology of Pavia (A.A., A.O., O.S., and A.T.)]; the Fondazione Cariplo (project 2018-2045; A.T., A.A., and A.O.); the Italian Institute for genomic Medicine (IIGM) and Compagnia di San Paolo Torino, Italy (G.M.); the European Community, Sixth Framework Program (PROCARDIS: LSHM-CT-2007-037273) (S.B.); the Italian Ministry of Health (Besta CEDIR project: RC 2007/LR6, RC 2008/LR6; RC 2009/LR8; RC 2010/LR8; GR-2011-02347041) (G.B.B.); "Progetti di Ricerca finanziati dall'Universita degli Studi di Torino (ex 60%) (2015)" (C.D.G. and G.M.); and ANR-14-CE10-0001 and Region Pays de la Loire (J.G.). G.H. was supported by a grant from the Wellcome Trust/Royal Society 098386/Z/12/Z. S.M. was supported by the Wellcome Trust grant 098387/Z/12/Z and 12284/Z/18/Z. This research was supported by the European Union through the European Regional Development Fund (Projects No. 2014-2020.4.01.16-0030 and 2014.2020.4.01.15) (F.M. and M.M.).